Zeality is mad now.
Okay, MY LIST TIME!
Chrono Trigger: First off, the story was too short. It did not go into depth on many of the finer issues that needed in-depth going into, like the nature of Lavos, the reason he came to the Chrono Planet, whether he was sentient, and so on and so forth.
Gameplay was too easy, and there were too many exploitable methods for making your party a powerhouse real quick.
Much of the dialog was cheesy and needed serious improvement.
Characters needed better development, and it needed a better translation. (Though that could not be helped given the situation Woolsey had to deal with.)
Chrono Cross:
The plot was done extremely well, but the pacing and exposition was so poor it made my eyes bleed, especially when you take into account how much atmosphere was provided.
The other main problem: the huge number of characters.
Look, I know why they did what they did, but this was not a game that you could just stick a character into in any situation. This is a game that focuses on a story surrounding specific characters and thus the game needed to be that way. Many of the characters should not have been in the game either as PCs or NPCs, and most of the PCs should have stayed NPCs where they were. Literally, everyone and their mother joined your party. It was nuts.
Also, a few things weren't done very well, such as the exposition at Chronopolis.
Other than those problems, though, the games were solid.