RD is just that now; a side story. When Kato first started working on it, he didn't even plan for it to be related to Chrono Trigger. He mentioned wanting to do a horror game, if I recall, but ditched that. By the time he finished it, he had tied it to the Chrono universe, but it wasn't meant to be referred to as the sequel. Kato seemed to do his damnedest to make sure that no one outside of Japan ever saw RD =P
I think possibly the next big thing in a Chrono game would be literal travel between worlds. Not dimensions, not necessarily time travel, but from one planet to another. The idea doesn't sound all that great as I'm say it, but it could happen. After all, when Lavos made his nest at Death Peak, there was several spawn. The final boss of CT and CC Lavos probably had its own mommy Lavos, that ultimately, if the party could somehow defeat the original one, they could save not just their planet, but many. I guess you could incorporate time travel too.
I donno, just me rambling...