We have to remember this was a time where text was still kind of expensive, so making the story more than barely coherent required losing enemy variety and such. The advantages of the switch to CD-ROM wasn't really the pre-rendered cutscenes, but the fact that there were no practical limitations to how much text you want to use. Every bit of text also lead to harder localization, which was still a part of the industry in its infancy.

So from where I stand, the coherence of Chrono Trigger is already kind of a miracle, given cart sizes