Ouch! and Vivisteiner, two members that I greatly respect, pretty much hit the nail on the head. I'll just throw in my two cents and reinforce that Kuja was probably the best villain from an analyst point of view (Kefka wins on sheer fun value, of course.)
As far as the battle, it's probably the most refined and polished that the ATB system ever got before becoming a clustersmurf. Load times don't really bother me in the slightest.
I still remember when I first started lurking these forums many years ago, this was THE black sheep of the series. I love that it's gotten more attention. My prediction is that either the FFII or FFIII fandoms are gonna spike next, then people will call those games overrated. Vicious cycle. Well, no matter what others think, this will probably always be my favorite FF for fun, silliness, amazing visuals (pre-rendered backgrounds, R.I.P.) and a really salient, touching plot.