It seems alot of RPG's of this generation have shifted towards having more depth of system and gameplay,but the stories pretty cliched. For example, pretty much all of the Atlus and Nippon Ichi ones have many many possible hours of gameplay (Atelier Iris, Makai Kingdom, Disgaea, Phantom Brave, La Pucelle, Stella Deus, etc.) but are pretty ho-hum in the story departments. There's also been a strong shift towards action as well... so there's a ton of also, fairly simple and/or cliched story action RPG's (Dark Cloud 1&2, BG Dark Alliance 1&2, etc.). I love a ton of RPG's of this gen, including most of the games listed, but it seems like after the massive amounts of epic RPG's on the SNES and the PSX, they've shifted towards having more engaging systems, and less on story (probably since so much has already been done before).
As others have mentioned, the Xenosaga games (1-2, 3 probably coming eventually) are pretty much nothing but story. The Shadow Hearts games (1-2, 3 coming fairly soon) get my top recommendation, as they are definitely my favorite PS2 RPG's. Star Ocean 3 also is pretty good story-wise, but it's an action RPG. I also highly recommend Suikoden 3, one of the best RPG's of the generation, though pretty rare and hard to come by, but stay away from Suikoden 4, it's pretty crappy. If Tales of Symphonia ever makes it to the PS2 in English, I recommend that, having enjoyed it thorougly on the GameCube. The Summoner games have their flaws, but they have a very rich game world, with excellent writing and a unique story.
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