Tokita says after the Final Fantasy VI development team finished with the sprawling RPG, they jumped right into building Chrono Trigger:

But was careful to note that despite ravenous fan interest in a sequel, prequel, or reboot, and his own desire to revisit the classic game in some way, that Chrono Trigger in many ways represents lightning in a bottle and may be off-limits since Square and Enix became one. 

We can still keep our fingers crossed for the future.