I am sure that the 3DS will focus on single-player modes such as a SSE story mode and the Wii-U will focus on multi-player modes such as online.
Maybe Wii U should focus on single player/story mode/single-player online and 3DS focus on online/local multiplayer? XD
Either way, I agree. And maybe that's how the two will work with each other. Maybe there will be console exclusive characters/stages and 3DS exclusive characters/stages, and you could link them up and use the exclusives in the other game modes.