Hopefully it's not tooo late to reply here...
Anyway, when this sort of topic comes up, my tendency is to recommend Live-a-Live, a little pearl by Square - it breaks away slightly from the usual RPG mold in settings and mechanics in a way I found refreshing.
As for setting, you don't get the usual medieval fantasy stuff - at least not at the beginning - instead, you pick from much less typical settings which all play a bit differently, each with its own protagonist: an old martial arts master in Fantasy Ancient China, a gunman in the wild west, a caveman in prehistory (fun detail, nobody actually uses words in this since it's in pre-verbal times - the speech bubbles use pictures instead), a futuristic setting where a guy with psychic powers eventually gets to ride a giant robot (complete with hot-blooded theme song at the beginning - you don't listen to actual lyrics, but get to see them in subtitles), a ninja in a(n optionally stealthy) mission in a huge fortress, a robot in a clautrophobia-inducing spaceship, and finally, as an interesting reference to the state of the games market back then, a present-day chapter which is essentially a fighting game using the game's own mechanics, with the perk that you get to learn some of your opponents' special moves. These different chapters can be played in any order, but you only move on with the bigger plot after completing all of them. Wich, by the way, involves an impressive recurring boss fight theme. (I'm trying to cut down on the use of the word awesome, I get the feeling that its recurring use will be the sort of thing the following decades ill make fun of about this one).
As for the battle system, I find it pleasantly dynamic compared to others for the same time - no concerns with things like MP or turns, you can move around at will in the battle grid, but every action you pick has a certain duration and area of effect - same with your opponents. Once a battle's over, you're fully healed again so you can go back to concerning yourself about the plot, not with cures or status ailments.
Only available through fan-translation, but totally worth it.
Other stuff I've been recently enjoying: Final Fantasy 5 (Dissidia made me curious about it, loving the job system in it and the Gilgamesh music) and Super Robot Wars 3 (bless fan translations; a nice way to get an introduction to shows I never watched and especially the rest of Gundam I'm yet to bother with; can be hard game though, it sometimes just removes or replaces your mechs and pilots without warning, so either hit GameFAQs or are very very careful about whom you level and what you upgrade).