I don't know if it's just me but I feel like Nintendo has put away their better Pokemon Spinoffs and have started to give us(what seems to be) these quick cash-ins instead. I've seen that the Spin-offs haven't been getting very favorable reviews.
Remember Pokemon Pinball? How tough it used to be to get every Pokemon, how you can go from having a really good game to everything just quickly falling apart? I think a new one would be perfect for the 3DS(and DS) considering the old one used to cut from the top to the board to the bottom often.
A New Pokemon Snap would be perfect for the Wii U in which you can the Wii U gamepad as the Camera. And with the 600+ Pokemon plus the new ones coming in I'd say one could be playing for hours upon hours.
Lastly Pokemon Puzzle League I believe would be a great fit for both the Wii U and 3DS. I mostly remember just button mashing in hopes that I did whatever I had to but recently I've seen gameplay footage of it and I miss it quite fondly.
What Pokemon Spin-off would you like to see make a come back?