As far as best RPG's go, I think Nethack wins. Sorry, had to go there.
I'd also like to toss the Star Ocean and Valkyrie Profile series in here. Not sure if it qualifies, but I'm a huge fan of Dark Cloud (Chronicle) and the Castlevania action/platformer/rpgs (SotN, CotM, OoE, AoS, ect ect) games. Can't think of any more off the top of my head, but there's probably a ton I'm forgetting.
Pokemon %@@!d half my childhood so I refuse to acknowledge it and the only good thing about FFX-2 was the job system, imho. As much as I love having a continuation to the FFX universe that's pretty much when square enix started this "cinematic experience" bs (ie. no gameplay). Not to mention the completion system for the game was so awful I still shudder remembering it whenever I see a progress rate on a save file.
I'd also like to draw attention to FFXII - Revenant wings. It's like an rts game without the strategy... or the game! It's one of the few games I've stopped playing halfway through (yes, I literally finished half the story line) and told myself "I don't care. I'm done." If it says anything I'm pretty sure Farmville was more engaging...