The reason he is so low is because he doesn't place high in tournaments. That's what the tier list is based of. Mewtwo is better than a lot of the bottom tiers, but he's still bottom tier.
Mewtwo is probably the hardest character to use proficiently because his moves aren't really efficient.
But why does he place low in tournaments, is the question. I don't think Pichu is used a whole lot more than him, yet Pichu is higher on the current ( outdated? ) list.
As far as I understand it, Mewtwo lacks two important factors: Approach and finishers. He's too slow to approach anyone except maybe with wavedashing, and even then his only combo starters are grab to down-throw to down-tilt or a straight down-tilt. Cue repeated down-tilts. And the only really strong attacks he has are the back-throw, which is powerful for a throw but still not all that great in most cases, and his very slow low-range down-smash. Well, and a fully charged shadow ball, of course.
He does have some good potential for combos, his tilts are great and all, but the lack of speed and especially the lack of priority make it too hard for him to approach another character once you reach a high level of play.
Then there's the fact that he's so easy to hit, combo and subsequently finish off.
So, on a certain high level, he might be potent if you're skilled enough, but once you reach a certain point, nobody using a half-decent character will let you approach safely.
Pichu at least has speed, and speed almost equals potential. Even if he's weak as hell, a good player can at least milk a bit of defensive and offensive strength out of the pure swiftness of Pichu.
And while Bowser is possibly even easier to destroy than Mewtwo, he at least has enough moves that allow him to kill, along with the up-b that elevates his offensive and defensive capabilities...
The one character whom I'd call worse than Mewtwo is Kirby, and Ness would be as well if it weren't for the DJC.