Chrono Trigger gets too easy during New Game+. I know you want to be uber powerful in case you want to fight Lavos as soon as possible, but it makes all the other fights boring, repetitive grinds. What were tough bosses on the first play-through can now be taken out simply by whacking them with a weapon a couple times.
My other complaints are exclusive to the DS version's new content. I mean wow, Square seems to have gotten lazy. The dimensional vortexes were made just by taking a bunch of rooms from other dungeons and throwing them in a blender. They do at least have original areas toward the end, and those play fine enough. But the worst area by far is The Lost Sanctum. It's just a bunch of fetch-quests that have you going up and down the same mountain over and over until you begin harboring a deep hatred for all mountains in existence. And I facepalm at the bridge area. They copy and pasted the bridge from Guardia Castle, which would be fine if the environments matched. The Lost Sanctum bridge is supposed to connect a cave over to a tower, but the cave entrance looks mysteriously door-like and carved into the side of another castle...huh. And why is this bridge encompassed in permanent nightfall when it's clearly daytime everywhere else in the Lost Sanctum?
Finally, the new ending. It raises more questions about Chrono Cross then it answers (And the last thing we need is more questions concerning that mindfuck of a story) and it feels more like a sidequest. Alright, so I beat up the Time Devourer, but what about the original Lavos, doesn't that still need to be resolved? Why are the credits rolling when the original threat clearly hasn't been stopped? Huh...I suppose I'll just have to imagine the group went immediately to the final battle after this fight, then.
But really, outside of the new DS content, the game is pretty much flawless in my eyes. Great characters, an engaging story, and a fun battle system make up the finest game I've ever played.