I have to pick between FF6 and FF8 for me Kefka's tower was interesting, plus the way you split into 3 parties which had to help each other was unique to that game, I believe (not like splitting into groups in FF7, and ignoring all but the first group which contains your strongest characters for the few last bosses) FF8's was nice because of the puzzles it contained, and how you had to go around unlocking your skills, should you feel th need to, although you could go fight Ultimacia without releasing them all if you wanted

I guess I'm biased towards the gameplay in final dungeons, judging from my choices - it's just standard run through and battle away as usual in the other games, even if they did have decent music like in FF5 (plus story when Gilgamesh appears for the last time), FFMQ, or FF7