Excuse me? I don't quite get what you mean by keeping your thumb on the analog stick? In other FF games, you keep your thumb on either the analog stick or the D-Pad, so what's the difference?
Anyways, the battle system is by far the most advanced. Buffs and Debuffs actually mean something, as they really don't in previous FF games. So you don't spend your whole time just going around auto-attacking (unless you decide you want to spend a full day just over leveling yourself at the start, which is just stupid).
I'll agree that they could have done so much more with the storyline and characters. A lot of subtle things happen though, that they probably could have made more obvious. Though I'm glad they didn't focus a lot on a love story (only hints and subtleties between Balthier and Ashe and the like).
I will disagree with your claim that VIII had a great story. The first disc was absolutely amazing, but it really just failed after that -- so many plot holes and no character development seen (if there was, it was forced). And the love story was incredibly forced and lame.
I don't think the storyline and character development in XII was that bad, it really just took a different route in the telling of than compared to other FF games where they follow this one guy that changes and saves the whole world, while meeting friends/love along the way.