I always admired Mewtwo and its power, it resides in my Top Coolest/Strongest Pokemon List. I actually prefer to use it over Arceus, simply since Arceus is godly, Mewtwo is a Pokemon. Arceus isn't just fair. Eventhough Arceus was based on a god, I still believe his stats are not superior, but they are rather Averaged. I loved Mewtwo more for the Incredible Special Attack and Speed.....I was simply shocked!
So anyway, Stat-wise(total), Arceus is better, however you can't really tell who is stronger in battle. I always will go with Mewtwo. Just give him at least one Clam Mind and its a sweep :P