I've got three MUs hot and ready.
Please note, these are subject to change. Correct me if I'm wrong.
Marth -
Mewtwo will, at first, not do so well with Marth. A lot of Marth's moves cause Mewtwo to fall back. You'll have to depend on racking up damage, do as much as possible. Against a Marth, you actually have really good chances staying alive if you offensive, as Marth is a defensive character, he'll try to keep distance. Your best chance at winning a quick stock is showing dominance. Dominance is key for beating Marth. Get lots of grabs, he can't use counter against grabs. Either throw him down for some good combos, or throw him back or forward. Once he's racked up more than 60%, fly him off stage! and gimp him. Do not be afraid to go near the boundaries of the blast zone, Mewtwo's recovery will help you get back on stage. Depend on using bairs when Marth is off stage, the distance your tail has will do well against countering his up-b. If you're on small stages with straight sides, like Green Hill Zone, you can do a stage spike and finish him off with a dair - it's really difficult to achieve though.
Roy -
Mewtwo's matchup with Roy is somewhat similar to Marth. With Roy though, his main game is either playing like an average Marth (very defensive), or being offensive. Mewtwo won't do very well with Roy, your best bet is spamming some shadow balls, and trying to grab him. Roy's moves, if correct, have a slight amount if ending lag to them, especially his shield-breaker. Use that ending lag to grab him or pull of a tail combo. Tail combos involve using various tilts, and finishing it off with either a bair, or another strong move. Once Roy has gained some percentage, take him off stage, like Marth! and play extremely offensive, defensive works too. Either gimp, or go near boundaries to push him to the blast zone. Do not wait until Roy is near the ledge to make your move, you'll be caught by his up-b.
Pikachu -
Pikachu, to me at least, is the worst match up for Mewtwo. You either succeed, or die trying very hard. If you simply use smash moves, you aren't going to do much. Pikachu can actually duck under the shadow ball, that includes a fully charged shadow ball, similar to how Kirby can. That's one move down. If the player has a fast reaction speed, something. competitive Pikachu player really needs, using side-b is useless unless you do it in the air, this also goes for down-b. That's all your special moves. For smash moves, your up smash has bit too much starting lag, but you should still be able to pull off combos. Side smashes work well, not the best. Your down smash should stay as a finisher move, especially when Pikachu is recovering with his teleport (up-b). Use tilts. Use tilts! I can't stress this enough. Use your tail too, any move involving Mewtwo's tail have a pretty good chance against Pikachu. Using your nair is also useful for grab combos, and getting some percentage on Pikachu. Stay away from his combo game, your best bet at winning the match is play a very good defensive game. Try to lure Pikachu off stage, Mewtwo's off-stage combat is very good.