The Final Fantasy series wanders all over the place quality-wise, though even the good ones are often no great shakes engine-wise. However, Final Fantasy Tactics is unlike the others, centering around a great little tactical system, and an interesting, involved plot. It's currently available for PSP and iOS, and has one of my highest recommendations.
Baldur's Gate I generally liked but stopped on because it kept bugging over which disk was in the CD-drive while playing it LAN. Plot was okay, characters were good. Main system had the advantage of being based on a solid RPG engine, and the disadvantage of being based on AD&D.
Of course, all of this is to point up the fact that there's just no reason why 'RPG' should equal 'shooter'. An interesting thing that occurs to me now, is that all these examples are party-based RPGs, which seem to have gone away too.