Even though my opinion on Twilight Princess tends to change a fair bit with time, one thing that has been consistent throughout is how anti-climatic the final boss felt the first time. Now, maybe anti-climatic wasn't the right word after all, but I probably expected the fight wth Ganondorf to be more like Ocarina of Time. I mean, when he takes on his beast form it's so impressive and I really felt like he over-powered me, like I had all odds against me. I think Twilight Princess sort of missed that, because while a swordfight is an interesting way to finish it off, it didn't really have that element of being over-powered by the enemy, at least for me I guess. =\
I later came to appreciate the game's ending for what it is instead of what I wanted it to be, but the swordfight with a human Ganondorf really didn't give that "against the odds" feeling that I had when I beat Ganon in OoT. As far as I can remember, that's pretty much the only thing I felt could've been improved upon in TP's final boss battle. The rest, including the cutscene before the horse-chase was pretty well done, I think.
As I said, I thought his final fight was kind of anti-climatic, but since they had already used his beast form, I guess it couldn't have gone any other way except keeping Ganon for the end, I guess.