Its a widely held belief that Obsidian games have top notch stories and gameplay, but their QA is....lacking.

Personally, I enjoyed NVN2 IMMENSELY.

As others have said, Dark Cloud 2 is widely considered a VAST improvement over the original Dark Cloud. Beter story, improved combat and town building systems, and more developed characters.

Tales of Vesperia, easily.

Three way tie between Dragon Quest 5, TWEWY and Sonic Chronicles.

Final Fantasy Xll

PlayBox39

You BLASPHEMER!

Sonic Chronicles

Etrian Odyssey 2

Izuna 1-2

Pokemon Mystery Dungeon 2

Pokemon Ranger

Devil May Cry 3, Okami, Godhand, and the entire Megaman X series (including Command Mission).

Tales of Vesperia.

SoTN and Order of Ecclesia.

Vesperia.