I think the controllers really hurt Nintendo's third party sales. See, the NES, and SNES, are great controllers, but in a way, very generic. All the face buttons are the same size, and the controllers were much more featured than the competion. ( SNES vs. three button Genesis)
However, in the 32 (64) bit gen, Nintendo made an off the wall, controller, so games like Tony Hawk 1 (2 and 3) controlled worse on the 64 compared to the generic dual shock (extension of the SNES controller and some PC pad made my EA). Also, the N64 had fewer usuable buttons than the dual shock. I mean the d-pad and L button were pretty much left alone. Basically, third party games controlled less than ideal, resulting in a lower quality game, and resulting in less sales compared to the superior Nintendo games where the controller fit the game like a glove. (Mario 64)
The same thing is happening the Gamecube. Who seriously buys SSX, or Tony Hawk GC versions unless it is the only console they own. These versions are inferior as the Gamecube is missing a button (call it z2). In SSX, tricks were removed from the GC version! I know I didn't buy these games.
If my hypothosis is correct, unless the Revolution sells like the NES, taking the world by storm with new innovative gametypes that appeal to the general public , then third party games will suck because the controller will prove too radical from the generic ps3 controller, and the games won't be fun to control. Only third party games dedicated to the Reveloution will stand a chance (like RE4 for GC) of having really good controls.
So I think if Nintendo wants to attract more 3rd party titles, make sure the Revolution controller is generic, and not lacking in features the competiors have (like buttons, and clicky thumbsticks).