So I did a topic a while ago about FF vs. other Square RPGs in which I sang Xenogears' praises over any FF I've played. Nevertheless, most of my "top Square games" list is composed of FF games.

This is mainly because I've only really played Final Fantasy games. However I did the same Final Fantasy vs. Other Square RPGs elsewhere and one guy didn't even list a single FF title on his list of Square's best.
I mean seriously, even if you restricted it JUST to the SNES, I'd still pick the Dragon Quest games, Chrono Trigger, Super Mario RPG, E.V.O, Illusion of Gaia, Terranigma, Soulblazer and a bunch of other stuff over the SNES Final Fantasy games.

If you restricted it to the PS1?
Valkyrie Profile, Star Ocean Second Story, Front Mission 3, Parasite Eve, Xenogears, Vagrant Story...

Playstation 2?
Robot Alchemic Drive, Valkyrie Profile Silmeria, Dragon Quest VIII, probably even the Kingdom Hearts games would rank a bit higher for me if you counted the Final Mixes, although the PS2 is the only one where it's even close.
This got me really interested in maybe finally expanding my horizons. I've been meaning to play a lot of these classic JRPGs for ages and maybe now I should get my butt into gear.

So...my question to you all is this.

Which Square RPGs of any generation have the best plots and characters according to you? I probably have a slight preference to SNES or PS1 era but PS2 is fine if any are applicable.