To parrot some others: Tactics Ogre, Vagrant Story, and just about anything created by Yasumi Matsuno gets my recommendation. The man has a knack for creating interesting, charming worlds with realistic politics and poignantly human issues. He also gets away from (most of) the typical jRPG tropes, which is always a good thing. Plus, he features good Shakespearean English in his games. Whoever does his english localization is a god.
Aside from that, Radiant Historia for the DS has the best time travel plot since Chrono Trigger. The Etrian Odyssey series, also on the DS/3DS, is nearly devoid of story, but it makes up for it with mechanical depth and a map drawing mechanic reminiscent of old school RPGs that you needed a pad of paper to properly play.
Aside from that, Radiant Historia for the DS has the best time travel plot since Chrono Trigger. The Etrian Odyssey series, also on the DS/3DS, is nearly devoid of story, but it makes up for it with mechanical depth and a map drawing mechanic reminiscent of old school RPGs that you needed a pad of paper to properly play.