Bgassassin on Gaf has said that the game from Retro is a new IP and aimed at the PS360 crowd. The Metroid - Star Fox crossover title was probably an idea that ended up on the cutting room floor so to speak. It makes absolutely no sense to have big hairy space marines, bounty hunters, pirates and Samus Aran in her bloody great big suit in the same game as furry, feathered and amphibian earth creatures that are walking, talking and flying in space ships from a pure design standpoint.
Retro will be working on an FPS or TPS game aimed at the hardcore demographic.
Not sure how I feel about the new controller, I really like the slide pad on the 3DS and the old design of the DRC had extra grips on them. I guess it may have been down to either Nintendo adding clickable functionality to them or feedback/requests from developers. The button placement seems a great deal better though.