More characters from Metroid, please!
Ridley is a must, being that he is a trademark antagonist from the series. Aside from that, he's very plausable - you could very easily gather all of the abilities he has from the series (fireballs, flamethrower, tail, claws, wings, etc.) and combine them into a conventional movelist. You could also give Ridley a transforming ability like that of Zelda/Shiek where he transforms into Meta-Ridley and makes use of all of the heavy artillery that he had in Metroid Prime.
This may be a bit of a stretch, but I wouldn't mind seeing the Mother Brain enter the fray, either. They could give her the T-rex body that she operated in Super Metroid (though downsized) and play as a relatively long range, defensive character with all of the weapons that she wielded. It shouldn't be too hard to fill in on the physical department, either, considering her shape.
Most of all, they need to give Samus a transforming ability. She has five or six different other power suits at her disposal from the entire series - it's time to put at least one of them to use. I'm thinking either the phazon or fusion suit, since they have the most unique abilities. She could have the phazon beam or, with the phazon suit, an absorption capability similar to that of Ness' energy magnet. Since the physique of each of the suits is different, they could also make her lighter, heavier, faster, or fall faster than she does with her regular suit in order to increase the distinction between her abilities between the two suits. With her regular suit, she could also use more of her traditional weapons, like the plasma beam.
Seriously, Samus has been by herself long enough. Let's put some of her old pals in there, shall we?