I think I've played Shaka and Fredrick the most out of all the leaders.
Shaka's awesome combos can be really addictive.
Fredrick had the traits and starting techs that I liked the best out of the existing Philosophical leaders at the time. I liked Saladin a lot in vanilla, but the trait changes completely screwed him over. I don't remember if Fredrick was Philosophical in vanilla, but I played him a whole lot in Warlords. Pericles is definitely cutting into the Philosophical leader pie for me, so he might be taking over soon.
I've tried to use Isabella on and off, but I always get really frustated by her combos. If I go early rush, the economy goes to crap, even with a shrine. If I play the build game, I still get surpassed in tech even though I'm doing every thing right. It really puzzles me.
In BtS, I've been playing a lot of Bootycall, Charlemagne, Pericles, and Justinian. Boudica just annoys me since everything else other than her traits are horrible, and they don't combo well at all. And with the improved AI for war, rushing with her doesn't seem to work out as well as it used to. Charlemagne is a beast. I have never finished badly with him. I always dominate the game when I play him. For some reason, my tech and economy are solid with him, and of course, the Rathus and Landsknecht just rule everything. My Pericles seems to have bad luck, as I can't ever seem to find metal at all, but otherwise, he's a powerhouse. Justinian I play like Charlemagne, but he's not as dominating.