Arceus is indeed the god pokemon of the pokemon world. In the anime, mangas, storylines, etc. he may be portrayed as the strongest pokemon of all. However, in the games, pokemon have stats. Arceus has some of the highest stats in it's overall abilities. However, what Mewtwo lacks in defense, he makes up for in insanely high attack stats. It can also learn nearly any move within the game, making it a very versatile opponent. Arceus may be powerful, but if he can't attack before Mewtwo, there's a very good chance Mewtwo can take Arceus out. In fact, more often then not, Mewtwo WILL beat Arceus in fights within the game. Mewtwo's Attack stat is only slightly lower than Arceus, his Speed is greater (meaning he'll hit first) and his Special Attack is far greater than Arceus', meaning he'll have a better chance to hit a critical, and his critical will be very, very deadly.
If you don't know that you're opponent is going to use a Mewtwo and don't use the proper plates on Arceus like Dark plate, then good luck defeating Mewtwo.