Am bored, so ganna list Factory Pokemon in the first 2 sets that I like and give reasons why (because let's face it, those are the 2 sets you will probably be playing most). I probably forgot a few and didn't list any Pokemon that I don't have experience with, so people who do a lot of Factorying feel free to
chime~ in with Pokemon I didn't list :) Also this list is only for Open Level because I personally find it more fun than Level 50.
Pokemon from battles 1-14 that I almost always take
451 | Flygon | Adamant | Yache Berry | Earthquake | Dragon Claw | Roost | Sandstorm | Atk/Spe
Amazing double stab, Roost, Yache, good typing/ability
485 | Garchomp | Jolly | Brightpowder | Dragon Claw | Earthquake | Double Team | Sandstorm | Atk/Spe
Same reasons as Flygon minus Roost/Yache plus Brightpowder/broken ability
583 | Gardevoir | Modest | Chesto Berry | Psychic | Thunderbolt | Calm Mind | Rest | SpA/SpD
CM+Chesto Rest and good coverage, plus it can set up against most special pkmns
382 | Gastrodon | Careful | Focus Sash | Waterfall | Earthquake | Recover | Mirror Coat | HP/SpD
Focus Sash+Mirror Coat :D Water/Ground types are just amazing in general in the factory. Recover is cool because you can switch into attacks, Recover off the damage and still have your sash for later. Overall a very cool Pokemon.
441 | Gliscor | Adamant | Yache Berry | Earthquake | Aerial Ace | Swords Dance | Baton Pass | Atk/Def
SD, double stab, plus it can Baton Pass out to another physical pkmn for some fun
608 | Gyarados | Jolly | Lum Berry | Waterfall | Ice Fang | Iron Head | Dragon Dance | Atk/Spe
There really isn't much to say here huh. Getting this at like battle 8 just gives you an amazing feeling inside :3
460 | Hippowdon | Impish | Persim Berry | Earthquake | Crunch | Slack Off | Curse | Atk/Def
Despite not having any HP/SDef EVs, I find this can take a lot of special abuse. Like Gardevoir, any physical Pokemon is free setup
361 | Infernape | Jolly | Coba Berry | Close Combat | Fire Punch | U-turn | Fake Out | Atk/Spe
Best lead Pokemon oof
453 | Jolteon | Timid | Focus Sash | Thunderbolt | Thunder Wave | Agility | Baton Pass | SpA/Spe
Another good lead cos Focus Sash + Speed passing. It and Magnezone1 are pretty much the only good Electric types in the first 2 sets, so I rarely pass up a fast Pokemon with STAB Tbolt like this one
474 | Kingdra | Timid | Razor Fang | Surf | Dragon Pulse | SmokeScreen | Rain Dance | SpA/Spe
Only if it has Swift Swim. If it has Sniper or if you don't know what it has, I still generally take it because of the whole double STAB/good coverage and good typing stuff, but if it has Swift Swim I 100% take it
459 | Lucario | Modest | Brightpowder | Aura Sphere | Flash Cannon | Water Pulse | Roar | SpA/Spe
STAB Aura Sphere is very nice, especially if you get it from 8-14 (because if a Pokemon has a Double Team moveset, it's usually the 2nd moveset). Lucario is just too good of a Pokemon :x
523 | Ludicolo | Impish | Leftovers | Leech Seed | Toxic | Double Team | Rain Dance | HP/Def/SpD
490 | Meganium | Calm | Big Root | Giga Drain | Leech Seed | Toxic | Substitute | HP/Def/SpD
606 | Tangrowth | Bold | Big Root | Giga Drain | Leech Seed | Toxic | Double Team | HP/Def/SpA
487 | Venusaur | Bold | Big Root | Giga Drain | Ingrain | Leech Seed | Sleep Powder | HP/Def/SpD
Didn't try these out until Glen mentioned Leech Seed/Double Team Grass types being awesome, and he's absolutely right
435 | Machamp | Adamant | Scope Lens | Cross Chop | Earthquake | Bullet Punch | Foresight | HP/Atk
Always take this cos no matter what ability Machamp has, it will benefit this set. Cross Chop generally tears apart enemy Pokemon
571 | Machamp | Adamant | Focus Sash | Revenge | Earthquake | Payback | Counter | Def/SpD
Got this the first time when all I saw was EQ and thought it was the first set. It's also awesome because of CounterSash
422 | Pinsir | Adamant | Coba Berry | X-Scissor | Earthquake | Rock Slide | Swords Dance | Atk/Def
What an awesome moveset :> STAB, quakeslide, Swords Dance, 2 good abilities
607 | Porygon-Z | Timid | Choice Scarf | Tri Attack | Thunder Wave | Recover | Trick | SpA/Spe
Glenscarfing: The ultimate strategy (also Scarf Tri Attack is pretty awesome if you don't have a set up Pokemon)
366 | Quagsire | Adamant | Rindo Berry | Earthquake | Aqua Tail | Brick Break | Counter | HP/Atk
Same thing as Kingdra really: I always always always take it with Water Absorb, but most likely take it either way because Water/Ground is a really good typing to have
483 | Salamence | Adamant | Cheri Berry | Dragon Claw | Aerial Ace | Aqua Tail | Scary Face | Atk/Spe
619 | Salamence | Jolly | Razor Fang | Dragon Claw | Fire Fang | Thunder Fang | Dragon Dance | Atk/Spe
I have the powerrrrrrrrr
423 | Scizor | Impish | Brightpowder | X-Scissor | Bullet Punch | Swords Dance | Baton Pass | Atk/Def
No explanation necessary lol. Even with Swarm this thing is so good
509 | Skarmory | Careful | Leftovers | Fly | Toxic | Double Team | Roost | HP/Def/SpD
Same thing as the Leech Seed/Double Team Grass types. This thing nearly always sweeps everything as soon as I trade for it
397 | Slowbro | Bold | Chesto Berry | Psychic | Surf | Calm Mind | Yawn | Def/SpA
402 | Slowking | Quiet | Shell Bell | Psychic | Brine | Yawn | Trick Room | HP/Def/SpD
Yawn is good in general on a bulky Pokemon like Slowbro/king, but the CM/Trick Room+double STAB is icing
359 | Swampert | Adamant | Shell Bell | Waterfall | Earthquake | Ice Punch | Protect | HP/Atk
495 | Swampert | Adamant | Lum Berry | Aqua Tail | Earthquake | Hammer Arm | Curse | HP/Atk
I've already said how much I love having a Water/Ground type in the factory, and Swampert just takes it to the next level
351 | Venusaur | Modest | White Herb | Leaf Storm | Sludge Bomb | Amnesia | Sleep Powder | SpA/SpD
This is another good Venusaur set. White Herb+Leaf Storm is very good,strang, and Sleep Powder/Sludge Bomb make it a very good set in general
464 | Walrein | Adamant | Chople Berry | Ice Fang | Aqua Tail | Swagger | Encore | HP/Atk
This is like the only Pokemon with Encore in Open Level, so I always take it because Encore is amazing and Walrein has really good defensive stats (I don't have my SkarmCents and BlissCents memorized yet but I bet Walrein has enough of them to buy a DS game!!)
440 | Weavile | Adamant | Chople Berry | Night Slash | Ice Punch | Screech | Fake Out | Atk/Spe
Second best factory lead behind Infernape1 :)
Other Pokemon that are good in the Factory's first 14 battles but aren't "mandatory" (I'm too lazy to put explanations for these ones right now but I'll probably edit them in later)
371 | Breloom | Impish | Focus Sash | Seed Bomb | Sky Uppercut | Rock Slide | Counter | Atk/Def
481 | Dragonite | Adamant | Lum Berry | Dragon Claw | Aerial Ace | Thunder Wave | Dragon Dance | Atk/SpD
432 | Drapion | Adamant | Lum Berry | Poison Jab | Crunch | Aqua Tail | Acupressure | Atk/Def
455 | Espeon | Timid | Lum Berry | Psychic | Reflect | Calm Mind | Baton Pass | SpA/Spe
372 | Forretress | Brave | Occa Berry | Gyro Ball | Bug Bite | Revenge | Counter | Atk/Def
466 | Lapras | Adamant | Leftovers | Aqua Tail | Avalanche | Ice Shard | Curse | HP/Atk
468 | Magnezone | Bold | Light Clay | Thunderbolt | Mirror Shot | Light Screen | Reflect | Def/SpA
484 | Metagross | Adamant | Brightpowder | Zen Headbutt | Bullet Punch | Facade | Light Screen | Atk/Def
620 | Metagross | Modest | Wise Glasses | Psychic | Flash Cannon | Shadow Ball | Sludge Bomb | Def/SpA
476 | Milotic | Modest | Shell Bell | Surf | Ice Beam | Attract | Hypnosis | HP/SpA
403 | Miltank | Impish | Cheri Berry | Return | Iron Head | Thunder Wave | Milk Drink | Atk/Def
413 | Mismagius | Modest | Kasib Berry | Shadow Ball | Power Gem | Magical Leaf | Memento | SpA/Spe
418 | Muk | Adamant | Black Sludge | Poison Jab | Shadow Sneak | Minimize | Acid Armor | HP/Atk
552 | Poliwrath | Adamant | Lax Incense | Waterfall | DynamicPunch | Poison Jab | Bulk Up | HP/Atk
482 | Tyranitar | Brave | Focus Band | Rock Slide | Payback | Avalanche | Curse | Atk/SpD
456 | Umbreon | Careful | Leftovers | Payback | Confuse Ray | Curse | Baton Pass | Def/SpD
425 | Ursaring | Brave | Focus Sash | Slash | Payback | Avalanche | Counter | HP/Atk
452 | Vaporeon | Modest | Brightpowder | Surf | Ice Beam | Acid Armor | Baton Pass | HP/SpA
582 | Yanmega | Adamant | Muscle Band | Aerial Ace | U-turn | Night Slash | Steel Wing | Atk/Spe
I love talking about the factory