Well, when I actually learned how to play the game effectively, I had only used a Mew out of the two. It had Psychic, its main attack, Rock Slide, for those that I'd prefer not to waste a Psychic on, Horn Drill, which was based on Speed instead of level at the time, and Softboiled, for healing both in and out of battle. At its peak level (which happened to be 87, due to internal battery conflicts), it still couldn't stand up to a L100 Mewtwo.
Of course, when you ask which one of the two is stronger, it hardly solves the problem to have both of them face different pokemon besides each other, because Mew & Mewtwo both have the power to completely annihilate anything else in existence besides each other, so I'm guessing this would be if the two were to face each other.
In that case, Mewtwo has both the ability to take many hits, and the ability to cheaply heal half its total HP, which puts Mew at a great disadvantage already, the only way out (aside from OHKO moves) being to create as similar a moveset as possible. Even then, you're just putting Mewtwo up against a weaker mirror of itself.
Mewtwo may not have as much of a variety as Mew, but you're forgetting that Mewtwo is still an insanely-powerful and merciless (spelling?) beast that can absorb nearly any attack and insta-heal it while killing everyone off, one by one, until it's the last one standing!
(As far as sprites go, Mewtwo's Yellow sprite is kinda awkward, in my opinion, so Mew wins!!!)