Gotta double down on Sephiroth. I've played some of the Final Mix exclusive bosses and the optionals from a few of the games, now, and the original Sephiroth fight is still the one I find the most challenging. It's probably also one of the most invigorating SquareEnix fights ever, because it really, really gives you a sense of just how powerful he is, which doesn't come across as well in even Final Fantasy VII itself.
Gonna have to agree with Sephiroth as well. I remember spending forever getting used to the mechanics. Practice makes perfect haha even though there's lots of cursing and moaning in between.
When I first played the first game at the original release, I couldn't get past the second Darkside battle (the one on Destiny Islands.) When I first played the second game, I had the hardest time with Grim Reaper, Demyx, and Xigbar.
