This could be, to some extent, a case of DS -> DSi. A "3DS 1.5", if you will. The DSi played (almost) all of the DS games, plus gave you some added features for games to take advantage of and a handful of exclusive games. It also gave us DSiWare, but that's a whole 'nother thing.
I really don't think that this is the future. With all the platform merging that Nintendo has talked about, I would suspect that we'll see a much greater connection between their *next* handheld and their next console, and probably a good bit of shared architecture, if they can pull it off.