Metroid and Metroid.
A Real Time Strategy game, similar to Starcraft and Command and Conquer, utilizing the strength of the Wii U touch screen controller. Emphasis on strategy puzzle solving, rather than Macro mechanics.
Personal answer would be Megaman Legends 3! (they saved bayonetta, they could save ML3)
Pull Retro off of whatever nonsense they are making and put them to work on Metroid Prime 4 IMMEDIATELY
I think most people want a Majora's Mask remake because of all the teasing of it. Ruby and Sapphire got teased forever and we knew it was coming.