Arceus, definitely. He did create the universe so it's no doubt he could wipe the floor with Godzilla.
Arceus created the Pokémon multiverse so is obvious that Godzilla would die horribly.
Arceus four limbs down. And Godzilla four limbs broken. FRA.
Combatants need to be at least Creator God level to be worthy to match THE Arceus. Not the one to be captured by us of course.