In response to giving Mewtwo his mirage attacks, i don't think that would be the best idea, particularly from Sakurai's perspective - Mewtwo can't learn those attacks, so it doesn't make sense for his Smash incarnate to be able to use them (and i doubt Game Freak would be too happy with a misrepresentation of one of their greatest creations)
and as for having only special-based attacks for his Pokemon moves, i'm all for that; but again, it would be unfair to represent Mewtwo as being physically incapable, seeing as [everybody just loves to forget that] his base Attack in the games is 110, which is more than beastly; nothing in comparison to his base 154 Sp.Attack, but Mewtwo is by no means weak in the physical sense - this reminds me, Mewtwo's base speed is 130, so if anything he should be fairly faster than his smash attacks are strong... if that makes any sense whatsoever?
Unfortunately, a proper representation of Mewtwo in any Smash game would drop him straight into God-tier (which is where he should be, in all fairness), and he would be less fun to play if there wasn't much of a challenge to using him
but here's what i would think a decent Mewtwo would be like (VERY basically):
Size: Large
Weight: Heavy
Speed: Fast, faster in air than on ground
Jumps: not sure really...
Fall: Slow, potentially with a levitate like Peach has
Neutral A: Weak
Smashes: Weak
Tilts: Weak, and not very much knockback
Nair: same as Melee
Other Aerials: decent killers
Neutral B: same as Melee, longer range fully charged and perhaps faster
Up B: same as Melee
Side B: Psycho Cut, or something along those lines - i like the idea of Mewtwo having a decent projectile other than his Neutral B
Down B: what about the psychic tornado thing he does in the manga? He can't move while he's in it, but he can only be reached from the top? Just another idea
Final Smash: as tempted as i am to say "Psystrike with a spoon!", which would be friggin awesome, i would LOVE to see the big explosion thing he does in the movies whenever he needs to get rid of Team Rocket; it wouldn't have to be as overpowered as it was in the movies, but it would be so cool to be able to do that in a smash game
also, i liked his rolls in Melee, and his ground-dodge should be probably be quite slow since he's an aerial character, but as much as i thought his airdodge was awesome in Melee i think it would be even cooler if Mewtwo didn't have an airdodge (since he has a similar Up Special anyway), but could make a shield in midair like in the films; the shield could be broken of course, in which case he'd tumble to the ground and then get his stun, but he'd also lose his airdodge so it shouldn't be too broken if at all? Again, just another thought.