Generally this kind of overhaul would most benefit early 3D (PS1 or Saturn) games that had low-res textures, camera angle and control issues. I thought the reissue of Jet Set Radio was fantastic. I always loved that game, but when they fixed the camera shit with the dual anologue stick and cranked up the frame-rate, it became a masterpiece, IMO. Loved it to death.

That said, here are 2 of my votes:

Ecco the Dolphin: Defender of the Future: Amazing game, totally ahead of its time, but was way too much for the Dreamcast to deal with. I put up with it 15 years ago, but now the framerate drops so bad it's unplayable.

Starflight 1 and 2 and the Star Control series: I know this genre is getting revived but I'd love to see these stories and these gameplay mechanics souped up to the level of Mass Effect. None of the modern space-opera games are funny. I always found these games hilarious.