I'd like to see Dark Cloud 2 remade for modern sensibilities. It's a classic as it is but there are a few ways it could be improved and upgraded. The combat could sure use a touch up. I think a spiritual successor would be more appropriate than a straight up remake.
I'd like to see a Director's Cut of Twilight Princess, with HD graphics (LIKE THE DEMO THIS TIJME, NINTY!) and all the story content that is so obviously missing. So Princess Zelda's role would be expanded with her appearing as Sheik and the Gerudo would be included which would provide means to explore Ganondorf's character further so he feels less like an 11th hour surprise guest star and more like an integral part. I'd also like to see more tie ins to OoT like they did with the Temple of Time with areas from that game appearing like Goron City making a return and even the dungeons from OoT returning as optional side dungeons. Storylines would focus more on side characters that don't get enough attention like Ralis, Illia, and the resistance gang. Oh and the Twilight Realm would actually feature as a whole other overworld like it should have been in the first place, with Link and Midna zapping back and forth and complete with its own line of dungeons, sidequests, towns, storylines, etc.
The original Mass Effect looked and played dated when it released. It would be great to give it a graphical overhaul and revamped mechanics. Better cover shooting, improved vehicular exploration, maps that aren't copy pasted from the same half dozen assets and configurations.
Skyrim.