I was thinking of writing a more comprehensive criticism myself, but for now I'm just going to bullet point it.
The final battle... I had the same problems as you. Let's just leave it at that.
However, I also had a lot of other issues with the game.
Like, why is nearly every facet of the final act derivative of one or more of the previous games? I find it a bit silly to fight a boss that looks like TP Ganon but is fought like TWW Ganondorf. Also, what's Nintendo's deal with main characters being possessed by evil demons as of late?
Furthermore, the game's ostensibly linear structure bothered me. Though it is not really worse than previous titles in the series, it is the first Zelda that is literally on-rails. It's like a dungeon crawler with a minigame between temples to break up the monotony. I was expecting something with a little more depth than that. Aonuma's original idea of creating the layout of the tracks would have been a great way to add some depth and variety to the game.
Another thing, I was hoping they would really make the most of having Zelda as your accomplice, but no. The train rides would have been a perfect time to build on the relationship between Link and Zelda, but instead she is simply reduced to the task of a lookout. I don't think it was all bad - there are some interesting things about her naive and self-indulgent nature as a child ruler - but I feel Phantom Hourglass was far better written, with a much more intriguing cast of characters. Perhaps the lack of Hidemaro Fujibayashi as writer/assistant director is to blame for this.
Naturally there was a lot I liked about the game. Many small improvements over PH. Overall though, there is no doubt in my mind which is the stronger game, and the sequel does not fare too well by my standards.
Essay Pro