Chrono Cross was a good game in its own right and it build on and adapted the systems in Chrono Trigger for the modern era. But it does seem like they're afraid of the IP. The only references to the original in the game are a guarded reference to Magus and the explanation of the final boss. And why would you make a sequel to a time hopping IP where you are unceremoniously stuck in time? All of which is okay, but then they drop the series cold because they need more time for....FFX-2? Running their MMOs? Does the top brass not even like the game?
Also seconding Vagrant Story. Another boundary pusher that was one and done for some reason. Its hard to find games that have that kind of love invested in every corner.