Thats my point: Some of the best FPS, RPGs, and such are usually based around the antithesis of their own genre cliches.
Best JRPG? Chrono Trigger (atleast imo), becuase it does away with a set world, and opens up multiple worlds and paths to victory and such.
IMO, I agree with the Saints Row comparison...Kind of. I would love to see a Saints Row-esque game (atleast in the driving, shops, and town layout), but make it like a KOTOR-esque ARPG, in the fact that it's strongly party based, laden with stats, and tactics. Operation: Darkness might wind up being kind of like that, but in a very strict linear-level sort of way.
And I also agree with the Shemmue comparisons as well - which was a good example of how a strong RPG story can be told in an urban setting (as well as the entire Midgard portion of FFVII).
But again, I just haven't seen anything that could a great seller: a GTA Sandbox game, but relying on strong RPG traits (like an Oblivion/GTA Third Person hybrid).