I'd like to see Legend of Zelda: Wind Waker remade with LOZ: Twilight Princess graphics. I did really like wind waker, and I think it would be taken more seriously if they hadn't made it look like a terrible cartoon. Although I would definitely like to play as a wolf in that game too, so they'll probably do that again instead. Maybe instead of that sailing portion of Wind Waker you could doggie-paddle to each island.
I've said these next three before, but I can't remember on what forum. Jet Force Gemini, especially now that we have online play and every controller has two analog sticks, or an analog stick and aiming remote, for proper shooter gameplay without a mouse.
Starfox, as it played inStarfox: Assault, the combination of being able to jump in and out of vehicles and updated on-foot controls would make this a nice online game as well I think. Having arwing battles in the skies over a ground battle at the same time would work nicely I think, since most multiplayer battlefield type games have restricted dogfighting-type stuff and it would be a nice mix, especially with different ships and multiplayer games, like instead of chasing the guy who captured your flag on foot, you would have an dogfight to shoot him down, or he could run away on foot. A new campaign with online co-op would be good too. Unfortunately, this would all have to be done by Nintendo, who have shown little aptitude for good online gaming, it would work so much better on Xbox or Playstation.
Lastly would be Megaman Legends, not necessarily the same storyline (in fact I might actually prefer a 3D shooter from the X series or Megaman Zero Series, or Megaman Zx series, since that's basically the same gameplay as Megaman Zero but with a weirder storyline), but a Megaman game 3D shooter, that, once again, would work a lot better with todays control scheme.
I guess the last three are all under the same category of stuff I enjoyed playing and would benefit from a modern day updates to control scheme and gameplay. One should note that aside from this I desired no real innovation, this might seem unimaginative or unambitious, and I'm definitely not against new game ideas, but sometimes just making the same thing only slightly better can still provide entertainment. If only the sonic team knew this...