The setup for these stats is simple: Assume every Pokemon has to do a heads up battle against every other Pokemon. It can optimize its EVs, item, moves, etc. for each match up, and knows which Pokemon it is facing in any given match up. A Pokemon is said to dominate another Pokemon if it can use a single set to beat all sets of the dominated Pokemon more than 50% of the time. For example: Crobat has Shedinja dominated. There is nothing it can do to block the following set up: Crobat @ Lum Berry - Aerial Ace. No matter what set Shedinja has or what strategy it tries to employ, it will always die in the first or second turn. A Pokemon is completely dominated if there is a 0% chance to win (as in the Crobat vs Shedinja example), rather than just a less than 50% chance.
These stats assume perfect play on both sides. Because prediction is never perfect, all actions must assume no knowledge of future moves. In other words, these scenarios are 0% prediction, 100% team building and long-term thinking. A dominated Pokemon must be dominated even if the player of the dominated Pokemon knows exactly what the other player will do.
Pokemon therefore have two measures. Pokemon dominate some number of Pokemon, and Pokemon are dominated by some number of Pokemon. One Pokemon is ranked higher than another if it is lower on neither scale and higher on at least one. If two Pokemon are ranked the same on both scales, they are tied, and if one is higher on one scale, but the other is higher on the other, nothing can be said about their relative ranks based on that data. Pokemon can therefore be ranked from 1 to 505 (alternate forms brings the total count up to 505), with some several Pokemon likely holding the same position.
This is not how real battles work, so they aren't really the best Pokemon, they're just the best for this particular metagame of 1v1.
1. Arceus ?
Arceus beats the following Pokemon: everything except for Darkrai and Mewtwo (503 Pokemon dominated)
The number 1 Pokemon shouldn't be a surprise to anyone. It has the obvious advantage of 120 all stats and a great move pool, as well as the ability to change types. If necessary, Arceus can use a Focus Sash against any powerful attacker and finish it off with Extremespeed, thanks to its 120 base Speed letting it go before most other priority users. There were only five Pokemon I considered as candidates for being able to beat Arceus. Groudon, Kyogre, Deoxys-A, Mewtwo, Darkrai. In my analysis, I have not been able to prove that Arceus can't beat Darkrai or Mewtwo, but I'm having difficulties finding a set that Darkrai / Mewtwo cannot beat. I've gotten close with Darkrai, but I suspect Mewtwo might actually be able to win. I put the question mark there because Mewtwo / Kyogre might be able to beat all but one Pokemon, and thus theoretically could be ranked #1 above Arceus. I doubt it, though.
Groudon: Arceus should use 192 Def / 192 SpA / 124 Spe Modest @ Chople Berry. The only move necessary is Grass Knot, but you might as well add Extremespeed. It will 2HKO even 252 HP / 252 SpD Careful Groudon (Rindo Berry is always 3HKOed). 252 Attack Adamant Groudon 3HKOs with its strongest attack on Arceus: Hammer Arm (it's a 2HKO with CB, but Arceus is faster and has a guaranteed 2HKO on CB Groudon). The Speed makes it faster than any non-Scarf Groudon. Scarf Arceus gets the 3HKO, but is 2HKOed, so the increase in Speed doesn't matter. Arceus should not be the Grass-type or Ice-type because then Groudon has stronger attacks in the form of Fire Punch (can easily 2HKO any Arceus, and threatens a OHKO against those that doesn't invest in Defense from CB Groudon) and Overheat (Overheat can also easily OHKO, meaning you have to be safe on both sides). Just stick with Normal Arceus and you have a guaranteed win.
Kyogre: Arceus should use 132 SpA / 252 SpD / 124 Spe Gentle @ Meadow Plate (with 25 a Def IV). The move set is Grass Knot, Calm Mind, Recover, Extremespeed. Arceus 2HKOs any Kyogre spread (252 HP / 252 SpD Calm) with Grass Knot, while Kyogre 3HKOs back with Ice Beam. Choice Specs Ice Beam is a 2HKO, but Arceus is faster. Rindo will turn Arceus's attack into a 3HKO rather than a 2HKO, but again, Arceus is faster. This means that Kyogre's best strategy is Icy Wind, Ice Beam, Ice Beam @ Rindo Berry, relying on Icy Wind's Speed drop to make Arceus slower than Kyogre. Grass Knot, Grass Knot, Extremespeed will always 3HKO Kyogre, with Extremespeed ignoring the Icy Wind Speed drop. Another possible strategy is Blizzard + Ice Beam but Blizzard's 70% accuracy shifts the required average damage up so high that Kyogre has a less than 50% chance to get it. The reason Recover is on there is to stop any tricky ideas with Avalanche + Rindo Berry, as a 252 Attack Adamant Avalanche 2HKOs Arceus. A single Recover brings Arceus nearly back to 100%, so it wins afterward. Calm Mind makes sure Kyogre can't use Rindo + Calm Mind to beat you.
Deoxys-A: 252 HP / 4 SpA / 252 SpD @ Spooky Plate. Judgment, Extremespeed. The best Deoxys-A can do to you is Psycho Boost, which you survive even if it has Choice Specs. You use Judgment. The reason you Judgement is that Deoxys-A might try something trick with a Chilan Berry and defensive EVs. Alternately, it could hold a Focus Sash, so you won't be able to OHKO it turn 1, anyway, so you might as well hit it with your strongest attack. In fact, Arceus can beat a hacked Deoxys-A with 252 all, +all nature, and Choice Specs + Ghost resist berry + normal resist berry (although you'll want to lower HP for some more SpA to guarantee this in the event of such a hacked Deoxys-A, the reason I didn't do that here is just so you can survive CHes from non-Specs Psycho Boost easier). The weaker version of Deoxys will also fail to such an attack.
Darkrai:
Mewtwo: I'm making no headway on this. Mewtwo is faster, bulky enough to take Judgement + Extremespeed from anything that can survive its attacks, learns Me First to screw with Ghost Arceus, and can set up Amnesia / Barrier / Will-O-Wisp to buy some extra time. I don't think Arceus can beat Mewtwo.
...
502. Shedinja
Shedinja can beat the following Pokemon: Beldum, Cascoon, Caterpie, Ditto, Kakuna, Kricketot, Magikarp, Metapod, Silcoon, Unown, Weedle, Wobbuffet, Wurmple, Wynaut (14)
Unown: Loses to Focus Sash + Bug Bite + Sucker Punch. Unown has no choice but to attack, so Sucker Punch is better than Shadow Sneak. Shedinja will has 252 Atk / 252 Speed EVs with a +Attack nature. This forces Unown to be faster than Shedinja (as two Bug Bites will OHKO Unown no matter what it does). Shedinja uses Bug Bite turn 1 (because Unown could hold a Jaboca Berry), doing at least 93 damage, assuming a Tanga Berry. The following turn, Sucker Punch will do at least 166 damage. Unown has 64 HP / 252 Def / 192 Spe Bold. This means that Shedinja will always OHKO Unown, as that is a combined total of 259 damage, and Unown can have at most 254 and still be faster than Shedinja.
Burmy with Coba Berry and Hidden Power Dark will beat Shedinja by just using Hidden Power Dark. The best Shedinja can do is Aerial Ace followed by Giga Impact @ Focus Sash, which fails to do enough damage thanks to Coba Berry.
Combee is faster and uses Ominous Wind twice @ Charti Berry to avoid Hidden Power Rock.
Magikarp loses to Agility, Protect, Bug Bite.
Every other Pokemon either wins outright or has the choice between using an attack and using Toxic. Shedinja cannot prepare for both and thus can't get a guaranteed win. I don't feel like calculating how many Pokemon fall into the "doesn't lose to or beat Shedinja" category.
503. Wobbuffet
Wobbuffet can beat the following Pokemon: Beldum, Burmy, Caterpie, Ditto, Magikarp, Unown, Wynaut (?) (7)
Anything faster than Wobbuffet can use a move like Toxic before it uses Safeguard. Anything with Leech Seed just uses that. This is the strategy for slower Pokemon:
Many Pokemon have more PP than Wobbufet has in non-damaging moves. They can just PP stall and then Wobbuffet loses to Struggle.
Other Pokemon learn Rock Polish, String Shot, etc. and can make Wobbuffet slower, then Toxic it.
Hippopotas: Sand Tomb and Slack Off. Use Toxic on low-level Wobbuffet. Substitute before attacking. Use Sand Tomb until it hits. Give Hippopotas a 0 Attack IV and Timid. Sand Tomb's end-of-turn damage + Sand Stream should be enough to kill Wobbuffet. Try and stay behind a Substitute at full health before attacking.
Clamperl: Icy Wind. Encore will fail, and Mirror Coat doesn't matter because that's the only shot Wobbuffet gets, so Icy Wind will never do enough damage to kill Clamperl, even with a critical hit. Follow up with Toxic. Add a move like Substitute or Aqua Ring to PP stall in case Wobbuffet opens with Safeguard to minimize wasted Toxic PP. This strategy also works with: Bidoof and Happiny. Makuhita, Torkoal, and Trapinch use a similar strategy with Rock Tomb. Lileep uses Constrict.
Metapod can use String Shot, Tackle, Harden, and Iron Defense to beat Wobbuffet with a PP stall. Tackle doesn't do enough for Counter to kill Metapod fast enough. Metapod should be able to intersperse Tackles with other moves to avoid being Countered to death.
Weedle, Kakuna, Wurmple, Cascoon, and Silcoon can String Shot and then Poison Sting on the turns Safeguard is not in effect.
The Ghosts use physical moves.
Kricketot can win with Growl, String Shot, Snore, and Bide. This gives it just as much PP as Wobbuffet (use a Leppa Berry to make sure), but you have the advantage of Bide taking several turns. Then Wobbuffet will Struggle itself to death. Even factoring in Choice Band Struggle with critical hits, a simplified calculation assuming Wobbuffet gets max damage on each Struggle shows that Kricketot has a 98% chance to win by starting out with Growl to ensure Wobbuffet can't pull something with Choice Band no PP ups Encore.
Combee gets Bug Bite and it learns Ominous Wind and Mud Slap. Both sides get the same amount of PP, and Wobbuffet will win the Struggle war more often than Combee (both sides use Leppa Berry), so Combee has to attack. For the sake of simple math, let's assume that Combee is able to get in 6 Mud Slaps without Wobbuffet hitting it with Mirror Coat, and it rolls 12 damage each time (max). Wobbuffet is down 72 HP. This leaves 4 HP / 252 Atk / 252 Def Wobbuffet at 450 HP. Now Combee's Bug Bites are doing a max of 78 damage with Insect Plate (no Life Orb allowed, thanks to all those Mud Slaps). This means that Combee needs to get in 6 Bug Bites without being hit by 2 Counters.
8.78% == chance no Counter will hit
26.3% == chance exactly 1 Counter will hit
64.9% == chance at least 2 Counters will hit.
In other words, Combee will generally lose in this situation. Now Combee has the option to lower the damage it does so that it can survive against 2 Counters, so Wobbuffet needs to hit it with 3 Counters instead! To do this, Combee needs to have an average damage of 65, assuming max HP. This means Wobbuffet will be able to take 7 hits. However, a smart Wobbuffet could raise its HP 6 points and then Combee needs to get in 8 hits, so I'll assume Wobbuffet has the following EVs: 28 HP / 228 Atk / 252 Def Impish. So Combee has to get in 8 Bug Bites without being hit by 3 Counters.
0.03% == chance no Counter will hit
15.6% == chance exactly 1 Counter will hit
27.3% == chance exactly 2 Counters will hit
57.1% == chance at least 3 Counters will hit
Combee still loses in this simplified scenario that highly favors Combee.
This means Combee has only one way to win: Mud Slap to reduce the chances of Counter working, Ominous Wind to boost Attack, and then Bug Bite to finish Wobbuffet off. More on this later
504. Wynaut
Wynaut can beat the following Pokemon: Beldum, Burmy Caterpie, Ditto, Magikarp, Unown (6)
Wobbuffet: My original thought was that Wynaut beat Wobbuffet, because it was slower and thus Wobbuffet lost to Struggle damage first. However, 4 HP / 252 Atk / 252 Def Adamant Wobbuffet does more than Leftovers heals to Wynaut, even with 252 HP / 252 Def Impish, whereas Wynaut does less than that to Wobbuffet, even with 252 Atk Adamant. This means that Wynaut dies at the end of the 4th turn to its own Struggle recoil, whereas Wobbuffet would die at the end of the 5th. Naturally, Wynaut also loses to all the Pokemon Wobbuffet loses to (I'm pretty sure... the lower defenses might actually get it a win with Counter).
Thinking about this more, I realized a few things. First: Charm makes all Struggle damage irrelevant except in the case of critical hits. Second: neither party can use Leftovers in this battle because Leppa Berry is so important. This means that draw mechanics are important. Does the slower Wynaut win in the battle, assuming no critical hits, or is it a tie? If it's a tie, I'll keep Wobbuffet ranked above Wynaut despite them having the same amount of "dominated" Pokemon, because Wobbuffet has a slightly higher chance to win against Wynaut factoring in critical hits, just not a greater than 50% chance to win.
505. Ditto
Ditto can beat the following Pokemon: none (0)
Ditto has to waste 1 turn Transforming, after which it only has 5 PP per move. This means Ditto will tend to Struggle first in the event of a PP war. Ditto copies all stats exactly, except HP. This means that Ditto will be 1 turn behind and can only make up for that by having more HP after taking a hit. Let's look at the Pokemon that have lower HP than Ditto:
Shedinja uses Focus Sash, Shadow Claw, and 0 Defense IVs with a -Def nature, as well as minimum Speed to guarantee Shedinja goes after Ditto Transforms.
Every other Pokemon with HP less than Ditto learns a non damaging move and can PP stall. With 252 HP / 252 Def Bold and 0 Attack IVs, every Pokemon takes less damage from CH Struggle than 25% (except Diglett, which takes exactly 25% max), meaning Struggle will always kill Ditto before it can kill you. The best moves to have are probably Rest and Substitute. These guarantee that even if Struggle gets a CH every turn, Ditto loses. Keep in mind that against Diglett, the worst case (in terms of low HP and Defense but high Attack), Struggle has to CH every single turn and roll max damage just to stay even with recoil, so if Diglett uses Substitute or Rest, it will survive that extra turn and win. Pokemon with at least Ditto's HP (Unown and up) get in the first hit as Ditto Transforms, and then the match is even (ignoring PP issues), meaning Ditto starts with a disadvantage, and is thus less likely than 50% to win.
The only two exceptions to this are the Pokemon that learn no damaging moves, Wynaut and Wobbuffet (above). They win by taking little damage from Struggle and having more PP. Recommended move set: Counter.
Unranked, but probably very low
Caterpie
Anything that can get 235 Special Attack can use HP Fire / Rock / Flying for a 2HKO, and they can hold a Focus Sash to make sure they get two hits, as long as they're faster than Caterpie (although they must watch out for Choice Scarf). Another good option is Tanga Berry to resist Bug Bite. This means only slower Pokemon and Pokemon that don't have that much SpA need to be concerned about anything Caterpie can do. Pokemon with 156 SpA can use Choice Specs and a 95 power STAB move for a 2HKO as well.
Feebas can spam Surf and get the 3HKO first (with smart EVing) or use Hypnosis. There is even the possibility of Flail. Choice items throw this off a bit, though.
Magikarp uses Bounce.
I don't think Pichu has Caterpie dominated, though. A Specs set dominates all Caterpie but Choice Scarf. Attempts to defeat a Scarf Caterpie make it lose to a Choice Band Caterpie. At least, I think. I didn't mess around with the EVs too much.
I'm pretty sure Caterpie has some of those low level psychics dominated, as well as Sunkern and Paras. However, there might be a clever way to use Counter to snatch the win. As long as Caterpie can beat at least 6 Pokemon (likely), it is still ranked higher than Wobbuffet. The real question is whether it's ranked higher than Shedinja.
Reference for anyone who wants to add to the lower levels of this list, the following Pokemon have extremely limited move pools:
Ditto, Unown, Caterpie, Metapod, Weedle, Kakuna, Wurmple, Cascoon, Silcoon, Beldum, Magikarp, Kricketot, Wynaut, Wobbuffet, Combee, Burmy
These stats assume perfect play on both sides. Because prediction is never perfect, all actions must assume no knowledge of future moves. In other words, these scenarios are 0% prediction, 100% team building and long-term thinking. A dominated Pokemon must be dominated even if the player of the dominated Pokemon knows exactly what the other player will do.
Pokemon therefore have two measures. Pokemon dominate some number of Pokemon, and Pokemon are dominated by some number of Pokemon. One Pokemon is ranked higher than another if it is lower on neither scale and higher on at least one. If two Pokemon are ranked the same on both scales, they are tied, and if one is higher on one scale, but the other is higher on the other, nothing can be said about their relative ranks based on that data. Pokemon can therefore be ranked from 1 to 505 (alternate forms brings the total count up to 505), with some several Pokemon likely holding the same position.
This is not how real battles work, so they aren't really the best Pokemon, they're just the best for this particular metagame of 1v1.
1. Arceus ?
Arceus beats the following Pokemon: everything except for Darkrai and Mewtwo (503 Pokemon dominated)
The number 1 Pokemon shouldn't be a surprise to anyone. It has the obvious advantage of 120 all stats and a great move pool, as well as the ability to change types. If necessary, Arceus can use a Focus Sash against any powerful attacker and finish it off with Extremespeed, thanks to its 120 base Speed letting it go before most other priority users. There were only five Pokemon I considered as candidates for being able to beat Arceus. Groudon, Kyogre, Deoxys-A, Mewtwo, Darkrai. In my analysis, I have not been able to prove that Arceus can't beat Darkrai or Mewtwo, but I'm having difficulties finding a set that Darkrai / Mewtwo cannot beat. I've gotten close with Darkrai, but I suspect Mewtwo might actually be able to win. I put the question mark there because Mewtwo / Kyogre might be able to beat all but one Pokemon, and thus theoretically could be ranked #1 above Arceus. I doubt it, though.
Groudon: Arceus should use 192 Def / 192 SpA / 124 Spe Modest @ Chople Berry. The only move necessary is Grass Knot, but you might as well add Extremespeed. It will 2HKO even 252 HP / 252 SpD Careful Groudon (Rindo Berry is always 3HKOed). 252 Attack Adamant Groudon 3HKOs with its strongest attack on Arceus: Hammer Arm (it's a 2HKO with CB, but Arceus is faster and has a guaranteed 2HKO on CB Groudon). The Speed makes it faster than any non-Scarf Groudon. Scarf Arceus gets the 3HKO, but is 2HKOed, so the increase in Speed doesn't matter. Arceus should not be the Grass-type or Ice-type because then Groudon has stronger attacks in the form of Fire Punch (can easily 2HKO any Arceus, and threatens a OHKO against those that doesn't invest in Defense from CB Groudon) and Overheat (Overheat can also easily OHKO, meaning you have to be safe on both sides). Just stick with Normal Arceus and you have a guaranteed win.
Kyogre: Arceus should use 132 SpA / 252 SpD / 124 Spe Gentle @ Meadow Plate (with 25 a Def IV). The move set is Grass Knot, Calm Mind, Recover, Extremespeed. Arceus 2HKOs any Kyogre spread (252 HP / 252 SpD Calm) with Grass Knot, while Kyogre 3HKOs back with Ice Beam. Choice Specs Ice Beam is a 2HKO, but Arceus is faster. Rindo will turn Arceus's attack into a 3HKO rather than a 2HKO, but again, Arceus is faster. This means that Kyogre's best strategy is Icy Wind, Ice Beam, Ice Beam @ Rindo Berry, relying on Icy Wind's Speed drop to make Arceus slower than Kyogre. Grass Knot, Grass Knot, Extremespeed will always 3HKO Kyogre, with Extremespeed ignoring the Icy Wind Speed drop. Another possible strategy is Blizzard + Ice Beam but Blizzard's 70% accuracy shifts the required average damage up so high that Kyogre has a less than 50% chance to get it. The reason Recover is on there is to stop any tricky ideas with Avalanche + Rindo Berry, as a 252 Attack Adamant Avalanche 2HKOs Arceus. A single Recover brings Arceus nearly back to 100%, so it wins afterward. Calm Mind makes sure Kyogre can't use Rindo + Calm Mind to beat you.
Deoxys-A: 252 HP / 4 SpA / 252 SpD @ Spooky Plate. Judgment, Extremespeed. The best Deoxys-A can do to you is Psycho Boost, which you survive even if it has Choice Specs. You use Judgment. The reason you Judgement is that Deoxys-A might try something trick with a Chilan Berry and defensive EVs. Alternately, it could hold a Focus Sash, so you won't be able to OHKO it turn 1, anyway, so you might as well hit it with your strongest attack. In fact, Arceus can beat a hacked Deoxys-A with 252 all, +all nature, and Choice Specs + Ghost resist berry + normal resist berry (although you'll want to lower HP for some more SpA to guarantee this in the event of such a hacked Deoxys-A, the reason I didn't do that here is just so you can survive CHes from non-Specs Psycho Boost easier). The weaker version of Deoxys will also fail to such an attack.
Darkrai:
At least that's what I used to think. Then I realized that Swords Dance Brick Break + Sucker Punch KOs Arceus, as does Nasty Plot Focus Blast. This has led me to rethink my plans. My current idea is max Speed on Arceus. This forces Darkrai to invest EVs into its Speed stat, thus limiting the amount of EVs it has to spread everywhere else. This is good for Arceus due to its high base stats, and bad for Darkrai, with comparatively weaker base stats. My moveset is Sleep Talk, Judgment, (X-Scissor, Extremespeed) @ Insect Plate. Arceus might need to invest in Attack EVs to use ES effectively, or in the defenses to take Dark Pulse / Rock Slide. My main concern with Sleep Talk, Judgment is that Darkrai might use Dark Void, and then Substitute. If I wake up on any turn other than the last turn, I won't know when to stop Sleep Talking, thus allowing Darkrai a potential free Substitute behind which it can Dark Void again, or just attack. Extremespeed will let me break the Substitute as I wake up, and finish off Darkrai if I need to. X-Scissor, therefore, is just to reduce the chances Arceus selects a non-Bug move with Sleep Talk.My old reasoning said:
Mewtwo: I'm making no headway on this. Mewtwo is faster, bulky enough to take Judgement + Extremespeed from anything that can survive its attacks, learns Me First to screw with Ghost Arceus, and can set up Amnesia / Barrier / Will-O-Wisp to buy some extra time. I don't think Arceus can beat Mewtwo.
...
502. Shedinja
Shedinja can beat the following Pokemon: Beldum, Cascoon, Caterpie, Ditto, Kakuna, Kricketot, Magikarp, Metapod, Silcoon, Unown, Weedle, Wobbuffet, Wurmple, Wynaut (14)
Unown: Loses to Focus Sash + Bug Bite + Sucker Punch. Unown has no choice but to attack, so Sucker Punch is better than Shadow Sneak. Shedinja will has 252 Atk / 252 Speed EVs with a +Attack nature. This forces Unown to be faster than Shedinja (as two Bug Bites will OHKO Unown no matter what it does). Shedinja uses Bug Bite turn 1 (because Unown could hold a Jaboca Berry), doing at least 93 damage, assuming a Tanga Berry. The following turn, Sucker Punch will do at least 166 damage. Unown has 64 HP / 252 Def / 192 Spe Bold. This means that Shedinja will always OHKO Unown, as that is a combined total of 259 damage, and Unown can have at most 254 and still be faster than Shedinja.
Burmy with Coba Berry and Hidden Power Dark will beat Shedinja by just using Hidden Power Dark. The best Shedinja can do is Aerial Ace followed by Giga Impact @ Focus Sash, which fails to do enough damage thanks to Coba Berry.
Combee is faster and uses Ominous Wind twice @ Charti Berry to avoid Hidden Power Rock.
Magikarp loses to Agility, Protect, Bug Bite.
Every other Pokemon either wins outright or has the choice between using an attack and using Toxic. Shedinja cannot prepare for both and thus can't get a guaranteed win. I don't feel like calculating how many Pokemon fall into the "doesn't lose to or beat Shedinja" category.
503. Wobbuffet
Wobbuffet can beat the following Pokemon: Beldum, Burmy, Caterpie, Ditto, Magikarp, Unown, Wynaut (?) (7)
Anything faster than Wobbuffet can use a move like Toxic before it uses Safeguard. Anything with Leech Seed just uses that. This is the strategy for slower Pokemon:
Many Pokemon have more PP than Wobbufet has in non-damaging moves. They can just PP stall and then Wobbuffet loses to Struggle.
Other Pokemon learn Rock Polish, String Shot, etc. and can make Wobbuffet slower, then Toxic it.
Hippopotas: Sand Tomb and Slack Off. Use Toxic on low-level Wobbuffet. Substitute before attacking. Use Sand Tomb until it hits. Give Hippopotas a 0 Attack IV and Timid. Sand Tomb's end-of-turn damage + Sand Stream should be enough to kill Wobbuffet. Try and stay behind a Substitute at full health before attacking.
Clamperl: Icy Wind. Encore will fail, and Mirror Coat doesn't matter because that's the only shot Wobbuffet gets, so Icy Wind will never do enough damage to kill Clamperl, even with a critical hit. Follow up with Toxic. Add a move like Substitute or Aqua Ring to PP stall in case Wobbuffet opens with Safeguard to minimize wasted Toxic PP. This strategy also works with: Bidoof and Happiny. Makuhita, Torkoal, and Trapinch use a similar strategy with Rock Tomb. Lileep uses Constrict.
Metapod can use String Shot, Tackle, Harden, and Iron Defense to beat Wobbuffet with a PP stall. Tackle doesn't do enough for Counter to kill Metapod fast enough. Metapod should be able to intersperse Tackles with other moves to avoid being Countered to death.
Weedle, Kakuna, Wurmple, Cascoon, and Silcoon can String Shot and then Poison Sting on the turns Safeguard is not in effect.
The Ghosts use physical moves.
Kricketot can win with Growl, String Shot, Snore, and Bide. This gives it just as much PP as Wobbuffet (use a Leppa Berry to make sure), but you have the advantage of Bide taking several turns. Then Wobbuffet will Struggle itself to death. Even factoring in Choice Band Struggle with critical hits, a simplified calculation assuming Wobbuffet gets max damage on each Struggle shows that Kricketot has a 98% chance to win by starting out with Growl to ensure Wobbuffet can't pull something with Choice Band no PP ups Encore.
Combee gets Bug Bite and it learns Ominous Wind and Mud Slap. Both sides get the same amount of PP, and Wobbuffet will win the Struggle war more often than Combee (both sides use Leppa Berry), so Combee has to attack. For the sake of simple math, let's assume that Combee is able to get in 6 Mud Slaps without Wobbuffet hitting it with Mirror Coat, and it rolls 12 damage each time (max). Wobbuffet is down 72 HP. This leaves 4 HP / 252 Atk / 252 Def Wobbuffet at 450 HP. Now Combee's Bug Bites are doing a max of 78 damage with Insect Plate (no Life Orb allowed, thanks to all those Mud Slaps). This means that Combee needs to get in 6 Bug Bites without being hit by 2 Counters.
8.78% == chance no Counter will hit
26.3% == chance exactly 1 Counter will hit
64.9% == chance at least 2 Counters will hit.
In other words, Combee will generally lose in this situation. Now Combee has the option to lower the damage it does so that it can survive against 2 Counters, so Wobbuffet needs to hit it with 3 Counters instead! To do this, Combee needs to have an average damage of 65, assuming max HP. This means Wobbuffet will be able to take 7 hits. However, a smart Wobbuffet could raise its HP 6 points and then Combee needs to get in 8 hits, so I'll assume Wobbuffet has the following EVs: 28 HP / 228 Atk / 252 Def Impish. So Combee has to get in 8 Bug Bites without being hit by 3 Counters.
0.03% == chance no Counter will hit
15.6% == chance exactly 1 Counter will hit
27.3% == chance exactly 2 Counters will hit
57.1% == chance at least 3 Counters will hit
Combee still loses in this simplified scenario that highly favors Combee.
This means Combee has only one way to win: Mud Slap to reduce the chances of Counter working, Ominous Wind to boost Attack, and then Bug Bite to finish Wobbuffet off. More on this later
504. Wynaut
Wynaut can beat the following Pokemon: Beldum, Burmy Caterpie, Ditto, Magikarp, Unown (6)
Wobbuffet: My original thought was that Wynaut beat Wobbuffet, because it was slower and thus Wobbuffet lost to Struggle damage first. However, 4 HP / 252 Atk / 252 Def Adamant Wobbuffet does more than Leftovers heals to Wynaut, even with 252 HP / 252 Def Impish, whereas Wynaut does less than that to Wobbuffet, even with 252 Atk Adamant. This means that Wynaut dies at the end of the 4th turn to its own Struggle recoil, whereas Wobbuffet would die at the end of the 5th. Naturally, Wynaut also loses to all the Pokemon Wobbuffet loses to (I'm pretty sure... the lower defenses might actually get it a win with Counter).
Thinking about this more, I realized a few things. First: Charm makes all Struggle damage irrelevant except in the case of critical hits. Second: neither party can use Leftovers in this battle because Leppa Berry is so important. This means that draw mechanics are important. Does the slower Wynaut win in the battle, assuming no critical hits, or is it a tie? If it's a tie, I'll keep Wobbuffet ranked above Wynaut despite them having the same amount of "dominated" Pokemon, because Wobbuffet has a slightly higher chance to win against Wynaut factoring in critical hits, just not a greater than 50% chance to win.
505. Ditto
Ditto can beat the following Pokemon: none (0)
Ditto has to waste 1 turn Transforming, after which it only has 5 PP per move. This means Ditto will tend to Struggle first in the event of a PP war. Ditto copies all stats exactly, except HP. This means that Ditto will be 1 turn behind and can only make up for that by having more HP after taking a hit. Let's look at the Pokemon that have lower HP than Ditto:
Shedinja uses Focus Sash, Shadow Claw, and 0 Defense IVs with a -Def nature, as well as minimum Speed to guarantee Shedinja goes after Ditto Transforms.
Every other Pokemon with HP less than Ditto learns a non damaging move and can PP stall. With 252 HP / 252 Def Bold and 0 Attack IVs, every Pokemon takes less damage from CH Struggle than 25% (except Diglett, which takes exactly 25% max), meaning Struggle will always kill Ditto before it can kill you. The best moves to have are probably Rest and Substitute. These guarantee that even if Struggle gets a CH every turn, Ditto loses. Keep in mind that against Diglett, the worst case (in terms of low HP and Defense but high Attack), Struggle has to CH every single turn and roll max damage just to stay even with recoil, so if Diglett uses Substitute or Rest, it will survive that extra turn and win. Pokemon with at least Ditto's HP (Unown and up) get in the first hit as Ditto Transforms, and then the match is even (ignoring PP issues), meaning Ditto starts with a disadvantage, and is thus less likely than 50% to win.
The only two exceptions to this are the Pokemon that learn no damaging moves, Wynaut and Wobbuffet (above). They win by taking little damage from Struggle and having more PP. Recommended move set: Counter.
Unranked, but probably very low
Caterpie
Anything that can get 235 Special Attack can use HP Fire / Rock / Flying for a 2HKO, and they can hold a Focus Sash to make sure they get two hits, as long as they're faster than Caterpie (although they must watch out for Choice Scarf). Another good option is Tanga Berry to resist Bug Bite. This means only slower Pokemon and Pokemon that don't have that much SpA need to be concerned about anything Caterpie can do. Pokemon with 156 SpA can use Choice Specs and a 95 power STAB move for a 2HKO as well.
Feebas can spam Surf and get the 3HKO first (with smart EVing) or use Hypnosis. There is even the possibility of Flail. Choice items throw this off a bit, though.
Magikarp uses Bounce.
I don't think Pichu has Caterpie dominated, though. A Specs set dominates all Caterpie but Choice Scarf. Attempts to defeat a Scarf Caterpie make it lose to a Choice Band Caterpie. At least, I think. I didn't mess around with the EVs too much.
I'm pretty sure Caterpie has some of those low level psychics dominated, as well as Sunkern and Paras. However, there might be a clever way to use Counter to snatch the win. As long as Caterpie can beat at least 6 Pokemon (likely), it is still ranked higher than Wobbuffet. The real question is whether it's ranked higher than Shedinja.
Reference for anyone who wants to add to the lower levels of this list, the following Pokemon have extremely limited move pools:
Ditto, Unown, Caterpie, Metapod, Weedle, Kakuna, Wurmple, Cascoon, Silcoon, Beldum, Magikarp, Kricketot, Wynaut, Wobbuffet, Combee, Burmy
