I consider Paper Mario 2 to be just as much a "real" Mario game as Super Mario Sunshine was. If you think about it, with the release of Paper Mario 2, Mario will have had more RPGs (3) than 3D platform games (2). Plus Paper Mario 2 definitly has more traditional Mario settings, characters, and music than Super Mario Sunshine did.
I suppose you could argue the only real "REAL" Mario games are the 2D side-scrollers. But in recent years, Mario has pretty much transcended genre. There are millions who know Mario more for games like Mario Party and Mario Kart than any of his platformers.
As for Miyamoto's controller comments.
I've longed believed Nintendo's next console would use some kind of motion-sensor technology in its controllers. Nintendo has already experimented with such technology before. In fact, the upcoming new Warioware for the GBA uses it.
Imagine a Mario game where Mario could actually jump higher if you gave the controller an upward thrust when pressing the jump button. Sure, something like that could get annoying if over-used but, in moderation, it could make the game feel much more interactive. I'm sure Miyamoto could think of dozens if not hundereds of other ways to utilize the technology in a Mario game as well. Of course there'd be much more traditional uses for the technology. Like using the controller as a steering wheel or flight yolk, essentially allowing the standard console controller to do many of the things an expensive accessory would.