The following is my opinion. It might not be true, but that's what I believe.
Square Enix has a variety of RPGs made by different people. One of them was the very well known Final Fantasy series. Another was the Chrono series.
The Final Fantasy series had a specific style of scenario. They were mostly unfamiliar with the players and put them in the plot without introducing them firstly.
Chrono Trigger was much more clear, specific and tangible. You started as a young boy in a familiar and ordinary world. That boy could be you, there were no secrets in his past, not something extraordinary about him.
Cross is something different.
The style of the story gets away from the CT style and approaches the FF style. The fans loved Trigger's plot because it was something different from the mass. When Cross was released, they probably wanted to see a game like Trigger, a game like no other. The plot of Cross, though, was kind of a usual RPG.
There is also the problem with the characters. In a Role-Playing Game, the character face situations, gain experiences and in the end of the story, they develop their personality. Since Crono and the rest, after defeating Lavos in Trigger were completed as characters, there was no need for further development.
Chrono Cross, although it wasn't like Trigger, is a great, G-R-E-A-T game.
-It contains the only sound tracks I know in a game that I can say are better than Trigger's.
-It has the only battle system I really enjoyed. The pokemon comparison has no base. Most battle systems in RPGs are based on weaknesses, colours, etc. The fact that each character has a colour, doesn't make them swallow. For example, each character's health is indicated by a number (HP). Does this mean anything about the character? No. It's simply required to calculate what happens in battles.
-It has touching scenes, more than Trigger did. In fact, in Trigger, all the world was beneath you and you weren't touched by war, despair, poverty. In Cross, you come closer to the characters. I wasn't touched by the people in 2300 A.D. at all, but I was touched by that little boy who's trying to find money to save his house.
-Anybody who says that the characters aren't well developed should think again. Serge is more developed than, let's say, Crono. What about Kid, Glenn, Harle, Lynx, Fargo and others? Of course, you can't expect all the characters to be developed in the same depth, but Razzly, for example, is not closely related with the main plot, so why should we know her past? And there couldn't be a different line for every character, in dialogues. This would mean 45 lines for each sentence, which would cause the game to be under development even until today.
-Not much relation with Trigger. Excuse me, is there any relationship between, let's say, the Finnish history and World War II? No. The Chrono world is large, exactly as our world is. You can't expect everything to be related with everything else - or at least, not so clearly. Cross is about a different story that shares some things with Trigger's story. That's for me the best point.
I don't think Square Enix will release any Chrono game in the next two years. Perhaps there won't be a sequel. If this happens, then the rest of the story is up to us