That would make them equals wouldn't it? And stop mixing the movie and the games like they are the same thing. In the game M2 is undeniably more powerful, and is tied with Lugia and Ho oh.
Expect with for in game my Venusaur can WTFpwn Mewtwo even though we see Mewtwo defeat hordes of enemies that would have taken down my Venusaur in the anime.
Meh. I take back what I said there, about the games being official just as well (not because of what you said though).
The games themself are actually more official/canon/relevant than the anime/movies are, because as a video game was how Pokemon started out (as you pointed out earlier), not as a movie or anime.
Then there's several reasons the anime and games are too different from each other to be compared well, but I'll just mention a couple:
1. The anime breaks the laws of balance that the games provide, by having things such as Pikachu KO'ing ground-types with electric attacks, Pikachu just being God-like overall (which is messed up), Water Gun made to look much more powerful/effective than it actually is, etc...
2. The anime makes too many contradictions to the game's storyline as well as several small parts of the game.
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As for the example you provided (about Jigglypuff KO'ing an Onyx at a much higher level), that just goes to show how inconsistent the battle system of most RPGs such as Pokemon can really be. Won't always have the same outcome every time...
Statistically though, Onyx is still overall more versatile than Jigglypuff. If you think Jigglypuff's a better Pokemon just because yours managed to survive against the odds once, then I guess I could say Bayleef's better than Dragonite just because mine was lucky enough as to KO a Dragonite after several Razor Leaf attacks one time.