Most 2D or sprite based games I feel would lose a lot of charm if they were remade in full 3D. Chrono Trigger, Symphony of the Night, Trails in the Sky, would probably be hurt by a remake I feel. Though there are plenty of them that should get some modern rereleases for accessibility purposes. SotN and Lunar really need PC releases for example, and CTs PC release still needs some fixing.
I think its mostly early 3D games that could use modern remakes, like Mario 64 or Mega Man Legends. Though some 2D games, like Sonic 2 ans S3&K would be nice in 3D most likely with Generations style gameplay.
Twisted Metal II
The Legend of Dragoon Definitely needs one. One of the best games of it's time with such a unique combat system but was overshadowed. The game has an amazing cult following and there are like 2 million signatures for a remake/sequel/prequel. One day I pray they will do it.
This'll never happen, but Shining Force 3 imo definitely needs a remake. This game was only released on the Sega Saturn, but it's supposedly one of the best and longest Shining Force games in the series with 3 scenarios. I've never been able to play it cause it's pretty expensive especially with most retro games. But man, I think it'd be an amazing game to remake. The music was done by Motoi Sakuraba for those who know his music, he's worked on the Golden Sun series, Star Ocean, and collaborated with Shinji Tamura with the Tales of games. The intro is pretty amazing though.
@Vero, Persona 1, 2, and 3 has already had remakes. They're on the Psp.