I got the very same disc, and I agree thoroughly. I love orchestra to begin with, so there's that. :P
Well, technically the tower collapses after you defeat Ganondorf the first time and he "dies," vomiting blood. And after you watch it collapse, Ganon bursts forth from the rubble. The battle is fantastic, with Zelda reacting to your damage and when you finally win, he dies realistically, with a stab to the head.
But, in my opinion, the TP one has so much more going on. You have to use the items you've collected after every boss to break through the barrier surrounding Hyrule Castle with a rather interesting cutscene, showcasing what the "true power" of Midna's ancestors is. You go through the castle, though with less interesting puzzles than in Ocarina, but with a tad more creepiness. Then you finally reach the final room of the tower, greeted by Ganondorf almost like in OoT, but no pipe organ this time. He gives you a little monologue, then possesses Zelda and uses her to fight you. So you have to attack the one you have to save. After finally finishing the repeat of OoT's first final battle, you go to fight Ganondorf in his primal form and make use of yours. Giant Boar with absolute magical control versus wolf and imp wth slight powers, sounds totally fair. Still, you win anyway. Thinking you've won, you approach Zelda, have a little chat, then are greeted by Ganondorf's Godly form. In which, Minda forces you two outside in an act of selflessness, the first one you actually see. She seemingly sacrifices herself, as even her ancestor's power is not enough to kill Ganondorf. You then are forced to fight him on horseback, all the while evading his ghost cavalryman and trying to hit him with a light arrow to spin attack him. Even then, catching him can be a challenge, and rightly so. After finishing that, he STILL gets up, and now it's a one on one duel, with you in total control of how you approach it. After finally winning that, you stab him through his wounded chest and he lumbers towards you with a sword dangling from his body. You save Mindna, see her in full form, and she destroys the only way for you to get to her when returning to her realm. It's a happy ending and a sad ending, all the same.
I agree that The Imprisoned sucked, but I really enjoyed fighting Ghirahim on all three occasions. So he makes up for it, if you ask me. Likewise, Skyward Sword is, chronologically, the first instance of the standard LoZ conflict, so Ganondorf will be in his original form. Just like Zelda was, and how Link was actually able to take control of the triforce, making him Godly as well. Skyward Sword did lack in some darkness, but... Zelda did kinda have her soul eaten, so we still had something. Too bad they went with Cursed Bokoblins instead of Re-deads, they filled the same role, but it just wasn't the same. However, the Silent Realms were pretty freaky, by times. Not in the fact of being scary, but the fact you're like "OH GOD, WHERE IS THE **censor** TEAR, JESUS I ALMOST GOT HIT, GET ME OUT PLEASE." Just adrenaline. I have got to say, though. The first time I fought Demise, he was a hell of a deal. I died way too much, I think. XD But it was so freaking cool to use lightning he summoned, coursing it through your sword, and throwing it back at him, finally defeating him just like in Twilight Princess. Still not top caliber, but good.