I'm still not sure how I feel about Chrono Trigger. I agree that the character backstories feel a little light; I'm quite late in the game, and it seems that characters like Ayla and Robo might as well not even exist. Their side stories happened so early in the game's chronology that they're forgotten by the end.
Chrono Trigger is really good, but I do find myself having to push through it at times (understatement of forever). Things come together after you get the Epoch, but there's still a lot of, "OK, now where the heck am I supposed to go again?" I think other games do a better job of keeping you on-track with some sort of hint system. More often than not, you complete a major chapter of Chrono Trigger and don't really know what to do next. Square Enix also had a nasty habit of having respawning enemies in areas in which you'll want to backtrack through, making doing so a chore.
At the same time, it always amazes me how the game crafts truly touching moments out of these little cartoony characters. It just goes to show you that dialogue and characterization trumps anything visual every time. Frog's regrets regarding Cyrus are truly sad at times, and there are several other instances in the game with thought-provoking statements from characters. It's excellent; perhaps not on the level of some of the best games in the Final Fantasy series, but nonetheless very well done.