I do agree with you, Kurt, with respect to the Castlevania games. The two PS2 games, and the one (or was it 2?) on the N64 are nowhere near as fun and timeless as SotN or any of the SNES and NES versions.
However, I think that there has been a fairly good transition for the Metroid franchise. I rather enjoyed both Metroid Prime and Metroid Prime 2. The former was also VERY highly rated, even when stacked up against games from the other 2 consoles. Granted, those two are shooters, but they still have the same feel to them as Super Metroid would (a wild claim, but they really do feel very "Metroidy", for lack of a better term). I wouldn't mind seeing, personally, what Super Metroid would be like using Metroid Prime as a model.
As for Chrono Trigger, while I do not think that anything can be done to make it better than it is (why mess with perfection?
), Chrono Cross, as a game standing on its own (ie: not compared to Chrono Trigger) was fairly well done. It wouldn't be a long shot to simply give Chrono Trigger a "facial" while keeping the gameplay and related elements the same. At the end of the day, though, my personal preference is to keep games like that as they are - I rather like the quaint charm of the SNES