So, Mewtwo's 'new form' is actually a Mega Evolution. Which are said to be temporary evolutions in battle only. So it's likely Mewtwo's Mega Evolution will not get any stat losses. Say, the implied loss of Attack and Defence for a boost in Speed. Many have suggested the 'old design' of Mewtwo would be a stronger, heavier but slower version of the character, and the 'new form' would be faster and lighter.
I think a Mega Evolution would be a great Final Smash for both Mewtwo and Lucario. Could see them both working slightly different though, Mewtwo's being more Super Sonic- like, and Lucario's being more like Wario-Man. Heck, Mewtwo's Mega Evolution could be similar to Diddy's or Yoshi's to. Just flying around, and blasting fools with Psychic blasts, but likely at faster speeds.
I'm pretty confident they'll use Mewtwo's normal design as a base character cause of this. Which is awesome. And now slightly more justified, cause with the Mega Evolutions Mewtwo isn't nearly as powerful as before in his universe. Kinda like how we have Ganondorf, Ganon in his human form, playable instead of Ganon (who is also a Final Smash). So yeah, this all bodes well for Mewtwo I think.