I kind of wandered into this discussion, and after reading all of the posts I figured I'd put my two cents in (well, more like two bucks really).
Mewtwo was easily one of my favorites from Melee and I was sorely disappointed when he wasn't in Brawl. Nothing says he NEEDS to come back. I feel that only the original eight can't be cut (yes I said eight, I'm not including the secret characters). Personally I hope he does though. But if he does he needs a lot of work.
I'm going to put a disclaimer here: I am NOT trying to offend anyone. Now, I think you guys might be taking the wrong approach in trying to figure out how Mewtwo would work best. Forget about the games he's in. The games aren't entering the fray, the character is. So let's take a look at him as a character. He's a genetically-engineered super-psychic with an attitude. He's super powerful and he knows it. To me that suggests field control. The others might be present, but Mewtwo knows it's His battlefield. This would allow him to feel as near god-tier as possible to someone that knows how to properly use him, while making him something of a glass cannon for everyone else.
Mewtwo's a big boy, so he needs to be a little heavier. But he needs to still be floaty as well. His running speed needs a boost, but his walk speed is fine. It gives him the look of being in control.
Mewtwo's physical attack is likely as good as it is because of psionic enhancement to his attack (his spoon is freakin' MADE of psychic energy!), so I'd avoid putting any real focus on those. Keep his physical strikes and combos more or less the same; perhaps a slight buff. Boost the power of his smash attacks a bit and maybe add Shadow Claw and Psycho Cut in there somewhere to make him a little flashier.
Keep Shadow Ball as his neutral-B, but give it a few tweaks. Keep it the same size as it charges and have him only use one hand, emphasizing how simple such things are for him. The blasts move at about the same speed as the shots from the Light Gun and each bursts with a small blast of psychic energy on impact. The longer the attack is charged the greater its range and the more intense the blast.
Keep Teleport for his up-B and leave it alone. It's range is perfect for warping between platforms mid-combat, making it not only a decent recovery move but also a valuable tool for controlling your own field position. At most maybe make it capable of doubling, like Pikachu's Quick Attack.
Change the side-B to Telekinesis. With this Mewtwo casually releases a near invisible wave of psychic energy from his hand that dissipates after a short distance or after hitting something. This attack will turn any projectiles it hits around, sending them back at the attacker AND INFLICTING DAMAGE. Additionally, if it hits an opponent it functions much like a ranged grab, letting him throw them as though he was standing right there. These throws are not as powerful as his normal ones, being weaker the further Mewtwo is from his target.
Change the down-B to Psychic. With this move, Mewtwo releases a round burst of power that affects characters similarly to Fox's Reflector. Unlike the Reflector, the burst doesn't stay when the button is held, doesn't reflect attacks and affects a somewhat larger area.
For his Final Smash, Mewtwo would have to use his signature move, Psystrike (despite how AWESOME it would be to see him use his spoon). This would have Mewtwo create a swirling cyclone of energy (much like the manga) that has range around Cook Kirby. Everyone in range would be drawn towards the center, where Mewtwo motions with his arms to create massive slashes that deal massive damage. The cyclone then dissipates, sending the opponents flying as Mewtwo auto-taunts.
Well, wow... Sorry this is so long, but here's my thoughts. What do you think?