Co-op, co-op, co-op! That's what I want! In fact, do a SMB3 style game with great level design and awesome new power-ups to match! New Super Mario Bros was great on both systems but I definitely feel it was lacking a few extra power-ups on both fronts. I'd be even happy with the return of a few classics (ie the Hammerhead Bros Suit and the lovable Tanooki Suit).
As far as the 3D platformers go, I'd be willing to play SM64 a third time if it had a devoted co-op mode for the main adventure. It was suppose to happen on the DS, but was scrapped and now honestly, with the 3DS, there is NO EXCUSES Nintendo. You can even do a remake of the Sunshine game or one of the Galaxy games, I don't care... I just want Mario & Luigi to stand side by side in an adventure so that me and my best friend(s) can kick Bowser's ass together!
MAKE IT HAPPEN NINTENDO! MAKE IT HAPPEN!!!