I've actually enjoyed the later FF games quite a lot as well, especially 9 for some reason. I really dug the design of that game, though the story wasn't all that interesting I suppose.
FFX was the game that first of the games made me feel a bit meh, and a lot of it had to do with the terrible voiceacting. None of the games are perfect of course, and they all have certain parts where I wanted to throw the game out the window. But I think they tell their stories in a pretty good way.
FFXII actually seemed to have a more intriguing story for me personally, but I couldn't finish it because it really felt like playing a MMORPG only single player. The combat was outrageously boring to me that I just couldn't bring myself to play past the combat areas. And I can usually suffer through crappy combat if there's a decent story in the game.
I'm currently replaying NWN2 for the third time, and for some strange reason I've enjoyed it more each time. I didn't think I'd ever play through it again after finishing it the first time. Thought it was decent on second playthrough, and now I'm actually quite enjoying myself. The game has some gigantic flaws here and there though.
I'm actually getting quite hyped for the expansion (which should be out in a month or two) after reading more about it. We're finally moving away from the Sword Coast and fewer companions that supposedly have more dialogues than the most developed companions in the main campaign (the expansion is shorter than main campaign).
The companions also don't seem to be your standard clichés (like many in the main campaign), but we have a Red Wizard of Thay, a hagspawn, a fallen cleric etc. A few of them written by Chris Avellone. 4 different endings depending on your actions throughout the game (not "choose an ending"), optimizations to the engine. A story that is more personal and dark.... The main thing I don't like is that we're moving into Epic levels, but I can live with it.