Well, I will warn people that this could be legitimate flamebait, but I'm gonna say it anyway.
FFVII was my first JRPG. Then, after a long while I found Chrono Trigger for the DS and figured it was worth the money. I DID in fact enjoy both. Chrono Trigger brought some actual design sense into some standard RPG mechanics that tend to outright fail in other games. For example, magic is powerful, standard attacks are not useless, and changing your armor out for the situation actually has a noticable effect (see my "5% fire resistance" article)
But no. It did NOT have a good plot. It had a HORRIBLE plot. Lavos wants to destroy the world. Don't get me wrong, FFVII could be said is just Find/Replace Lavos->Sephiroth, but there's reasons behind it, there's plenty of other things going on, and since so much screwed-up stuff is going on, they take adequate time to explain it.
There were legitimately times in Chrono Trigger when I had no idea what my party was doing or where we were going. I fought my way through to Magus because I couldn't find anything else significant on the world map. I found Robo in my first trip to the future because there was nothing else to do. There were even times when I forgot where I had last been and just sort of wandered the ages looking for an NPC who would say something different. And then when I finally get to some potential plot exposition, they barely answer any questions and just said "keep doing what you're doing."
Heck, I could have avoided the whole part of the game between fighting Magus and joining him if my characters had paid more attention to exposition, with a simple;
"Hi, evil overlord. Who the heck are you and what are you doing with these ritual circles?"
"Why, I'm trying to destroy an evil menace that will take over the world at some point."
"Oh, I see! Let us help."
FFVII played things straight; Perhaps by having too-long cutscenes, but they were still pretty easy to appreciate, especially the 3D-rendered FMVs.