The WiiPointer (as it's apparently called) already resembles the NES controller, and if memory serves, the TurboGrafx 16 controller. If they ever get Master System games too that should be adequate.
For the other systems there's a "classic controller". I don't see why they couldn't have just put a Select button on a wireless N64 controller. But maybe it has two analog sticks in case they can secure the rights to some PlayStation games? (Depending on the rights, I don't think it's an impossibility - I mean, Castlevania: Symphony Of The Night is coming to Xbox Live Arcade, so why not?)