I'm gonna open these cans of worms in this thread, hope you all don't mind!
Chrono Cross
Apollo Justice
Both of these games are fine in their own right, particularly Chrono Cross, but by including characters from the previous games detract from the original's resolution. Apollo Justice especially would be a good game (minus 4-3) if Hobonix just... wasn't Phoenix. Chrono Cross makes it impossible to play the original with the same sense of optimism because of what you learn of the fate of some of its characters.