Funnily enough, Puppet Ganon didn't give me much trouble. I thought he was one of the most fun bosses in the game, followed by Molgera.
I struggled a little on Jahalla, though. In the Earth Temple, I was always a little slow reflecting the light onto him, but in Ganon's Tower I had no problem.
It took me a while to lay the finishing blow on Ganondorf, and he kept on hitting me. I almost died twice.