Each stage was different in terms of difficulty and feel for me, so let me break this down.
Puppet Zelda: 1
Her attacks were incredibly easy to dodge, and the Dead Man's Volley was really easy if you had enough distance between yourself and Zelda, and she charged that ball so slowly you could run to the other side of the room if you needed to.
Beast Ganon: 3
Admittedly, I forgot how to stop charging beasts since I took a major haitus in the middle of the game, and thus had a great deal of trouble trying to remember the mechanics of how to stop rampaging monsters. Beyond my failure at the controls and the occasional annoyance of being unable to find his portals, the fight was still really easy.
Horseback: 4
Zelda took too long to shoot and Ganondorf really seemed to like swerving around the field. I also had some issues at first where he would charge me before I could get Epona into gallop. Overall, I'm just terrible with horseback fights; my coordination with Epona just sucks really.
Ganondorf: 3
As much as I loved this final duel, it was just too easy, like every other one-on-one fight in the game. Ganondorf could block pretty well, but it's really easy to dodge most of his attacks too. The chance thing was interesting, killer on the fingers but a piece of cake if you decide to use two hands to save your thumb muscles some strain. But still, one-on-one fights in general are cakewalk and only Ganondorf's high block ability and occasional guard-breaking fancy sword-work merited any difficulty.
Final score, I guess I'd round it off to a 3.