I would agree that Project M does it best. The Morph Ball crawl, the new roll, the ice mode, charging in the air, etc. It's all very nice!
Personally, even though I'm comfortable with her classic play style in Smash, I wouldn't mind a redesign. Like Mega Man, I feel she should play like she does in her games, being quick, agile, and having a lot of firepower. I'm not saying make it just like Metroid, though, because then her sheer firepower would be OP. lol
Samus has also proven to be monstrously strong, something that Smash fails to reflect. I know, I know, "balancing", and all that good stuff, but maybe to balance out her quickness and firepower, have her melee be slower and more deliberate akin to Ganondorf? Like, her weapons are good for zoning and dealing damage, while her melee is more risky but serves as her best way to score kills?
I mean, c'mon, she throws this giant lava whale into a wall and kills it. You have to admit, it would be an awesome feeling to have better throws and stronger melee moves.
Oh, and there's this feat from a manga. Not a canon manga per say, but... hey.