Okay, so after almost 4 weeks of ignoring the game, I decided to play again, and beat it tonight, after putting ~45 hours in.
The Zant battle was AWESOME, but ultimately way too easy. I lost about 2 hearts. It would've been nice to include every dungeon boss, because the Desert and Sky bosses were noticeably absent.
I'm glad the Fused Shadows came back into the story. It bothered me how they were taken away without getting to use them.
Fighting Zelda was weird. And way too easy. I could NOT figure out how to attack Ganon once I was in wolf form. But once I did, that became a lot easier. I liked the swordfight as the final battle. That's how it should be. Not some giant monster with a tiny weak point. Just two evenly matched opponents with weapons.
I still hate the camera. If a game requires platform jumping, it should also have a completely manipulable camera.
The weapons from dungeons 4 and 5 weren't used nearly enough throughout the game. There was a lot of potential for them, too.
The story still makes no sense to me. I still think Ganondorf came out of nowhere. Zant was a good villain. He made sense. Until you get to him, and there's this cutscene with some god, and then I was completely lost.
I think Majora's Mask is the best Zelda story-wise, because it's simple. You know you're going against Skull Kid from the beginning. You know you have to keep the moon from falling. It makes sense.
But Twilight Princess was just confusing. Collect the Fused Shadows, WITHOUT KNOWING WHY, then LOSE them! Then collect mirror pieces. Then go inside the mirror and fight a villain who no longer makes sense. Then fight the actual villain, who is only there for tradition's sake, and have the mirror be DESTROYED. What was the point of continuing with the game after a certain point? The world didn't stop because Zelda disappeared. There was no sense of urgency, much unlike Majora's Mask and even OoT.