This is a really cool thread, I thought I was the only one who thought of this kind of stuff!
I tried to do a hard one (Rayquaza vs Kyogre), but I went nowhere with that, so here's an easier one: Mewtwo vs Groudon.
With a spread of 214 Def/252 SpA/44 Spd and a Modest Nature, Choice Specs Mewtwo easily 2HKOs all Groudon (even 252 HP/252 SpD Careful ones equipped with a Rindo Berry) with Grass Knot. In fact, Groudon would need 164 HP / 252 SpD with a Careful nature (or any EV spread with a Rindo Berry) to avoid the OHKO (and this is assuming Mewtwo hits minimum damage output). Since this Mewtwo spread outspeeds all non-Scarf Groudon, the only Groudon sets that have even a CHANCE of attacking Mewtwo are:
- Any Groudon set with a Rindo Berry (the "worst" being an Adamant 252 Atk EV Groudon)
- Any Groudon set with at least 164 HP/ 252 SpD and a Careful Nature (the "worst" being 164 HP/92 Atk/252 SpD w/ Choice Band)
- Any choice scarf Groudon set (the "worst" being 164 HP/92 Atk/252 SpD with a Careful Nature because its the strongest Groudon set that can attack twice with Earthquake)
The first Groudon set gets a maximum of 278 Damage with Rock Tomb followed by Earthquake. Mewtwo has plenty of HP and precedes to KO with Grass Knot.
The second Groudon set does a maximum of 255 with Earthquake. Note: Life Orbed Rock Tomb + Earthquake would be stronger, but Groudon has so little HP after the first Grass Knot that it would die from recoil (even max HP/max SpD). I'm assuming Soft Sand EQ + Rock Tomb is approximately the same as Choice Banded EQ. Even then, Mewtwo has 353 HP so it would survive.
The third Groudon set does a maximum of 342 damage with two EQs. Close, but not enough (Mewtwo has 353 HP).
EDIT: A Paraflinch set is also threatening, the "worst" being the 252 Atk Adamant Groudon w/ Rindo Berry from the first set. However, it would take two Rock Slides + an EQ to KO Mewtwo, a 20.4% chance of two flinches factoring in the accuracy of Rock Slide (that's like a Hydro Pump missing). Combined with Mewtwo rolling absolute MINIMUM damage with Grass Knot, the probability of this is EXTREMELY LOW. I mean, the chance of a critical hit is MUCH higher, and we seem to be avoiding that chance in all of the previous "proofs." However, if you guys want to try some sort of Lum Berry set so that Mewtwo avoids being paraflinched, go ahead.
EDIT2: Actually, 252 HP/252 SpD Careful nature Groudon w/ Choice Scarf has the best chance of KOing Mewtwo by using Fissure (49% it hits at least once, NOT INCLUDING the chance of Mewtwo rolling NEAR MINIMUM damage with Grass Knot). However, I'm assuming OHKO clause is in effect.
Therefore, Mewtwo dominates Groudon.
Q.E.D (<- I feel like such a Mathematician saying that!)