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My long-held opinion (that's also the only right one) is that for Pokemon, especially legendary Pokemon, battle power and magnitude of their influence on the world is two entirely different metrics. Like, a rampaging Gyarados can destroy entire villages just by being a huge destructive snake with elemental powers, and an Onix probably could too as long as there's no sprinklers involved (and a Milotic, in turn, could calm both without even battling them); however, neither is a better battler than an Ursaring (which is peaceful in its pokedex entries, would probably do less damage even if it went on a rampage, and has no elemental powers) or a Medicham (which has its powers mostly revolve around using psychic senses to augment its USE FIST and DODGE IT options).
I mean, that's really the only way Arceus makes sense in-game. The Sinnoh Trio and Yveltal, too.
So when the scientists tried to make the world's most powerful Pokemon, they did succeed — in the battling sense. Arceus IS a being capable of creating universes and remaking lords of time and space, in its own deific ritual-casting way; and Giratina can, in the right circumstances, just NOPE any given Pokemon into the Distortion World. BUT when it comes to "both of them get into a ring and dish it out, using their powers WHILE trying not to get hit by enemy's, until one of them faints from the beating or exhaustion", Arceus just isn't that much of a fighter. In it's plateless state (which notably is actually BETTER at fighting but is stated as weaker lore-wise), there's a real (and pretty decent) chance that Arceus' overestimation of its powers and lack of combat experience will conspire against Him, and Mewtwo that awakened an aura sense in addition to its psychic powers (i. e. got that sweet Aura Sphere, which IIRC it now learns on a level-up), being a born and made combatant, will beat Him into the ground with less trouble than it would have against Mawile.
See also: Superman vs. literal god Darkseid.
