There's an interesting thread over on Neogaf titled Has Chrono Trigger REALLY not been topped yet?
Chrono Trigger is an excellent game that did a lot right but there have been plenty of articles on why Chrono Trigger is a great game. Here's an article on where Chrono Trigger could have been improved.
1. Character Customization. Quite simply, there really isn't any character customization other than a simple equipment system. Most other RPGs give the player some control over how to build their characters, but Chrono Trigger features very linear individual progression. This is made up for somewhat with being able to choose who to stick in your active party & the multi-character combo system but it's still the weakest aspect of the game. Now, it's true that some players prefer highly linear character progression in their RPGs (see Final Fantasy IV's huge popularity), but it is possible to give each character their own unique gameplay feel while still letting the player have some say in how they grow and develop over the course of the game. For a great example, see Persona 4 - the main character is a blank slate for the player to create, whereas your allies have more linear progression (although even there, you do have some say in how they progress, especially in P4G).
2. Localization and writing. Chrono Trigger's writing wasn't anywhere near as bad as your typical SNES RPG but even at the time, it was nowhere as good as say the writing in Lunar: Eternal Blue (which came out the year earlier on the Sega CD) or a well done PC RPG or point & click adventure game from that era. And these days, the writing in games from companies like Atlus & XSeed Games far exceeds the kind of localizations and writing we got back in 1995.
3. Tech limitation. This should be obvious but technology has progressed substantially since the SNES days. Even on the portable systems, you could make a game with a similar aesthetic to Chrono Trigger look much better now. If nothing else, games can be much bigger than 4MBs allowing for much more variety of visuals (Chrono Trigger looks great but several dungeons use palette swaps of earlier dungeon tilesets due to space limitations).
4. Names. A frog named Frog? A robot named Robo? They seriously couldn't come up with anything better than those?
5. Endings. It was very neat that you could Chrono Trigger has multiple endings at a time when most console RPGs did not. However, most of the endings in the game could only be obtained by replaying the game in New Game+ mode and ending the game at arbitrary points. It would have been much better if the endings were more organically reached through the course of a regular playthrough.
With all that said, some of these "flaws" are pretty minor. It may not be perfect, but Chrono Trigger remains one of my favorite games of all time (though not the favorite) and is one of the games that we have been studying extensively to learn how we can become better RPG developers.