In-game: Mewtwo, Aura Sphere is enough to explain why
Anime: Arceus. First off, Arceus can negate any attack by switching types on the fly. Second, no a mount of sheer power can take down Arceus, shown where he take A REAL LIFE METEOR TO THE FACE. Not a Draco Meteor, the real thing. Offensively Arceus is also god-like, spamming no-recoil Hyper Beams.
Actually Mewtwo has a solid chance against Arceus, since he's the only Pokemon Arceus didn't create (humanz made it) so Arceus has no power over him. Mewtwo's still not powerful enough to take out basically God head-on, but I think he's smart enough to find a way to trick Arceus or something