This is one of those movies that I really should have seen, but hadn't until very recently, and I must say, it was amazing, except for one little thing... From watching it, I have concluded that it is two movies shoved into one. The first is dark, complex, and probably not for children. The second is a lighthearted and comedic children's movie based on a book which is none of the above. My guess is that it began as the former and bits and pieces of the latter were shoved in when someone realized that they were making a Disney movie and hastily removed some of the less family friendly aspects and replaced them with amusing animal/statue sidekicks.
I know I am not the first to complain about it; the gargoyles are a pretty glaring addition. Paris is burning to the ground and they start singing about how Quasimodo is totally going to get the girl. It's terrible mood whiplash and doesn't fit at all with anything else in the movie, they've even got a completely different look to them.
What I believe happened is that initially, Quasimodo walked the line between human and monster, at least more-so than in the movie we got, where he's as good as a saint. In particular, Frollo calls him monstrous in "Out There" but it never goes anywhere. Also, there is one shot during the "siege" of Notre-Dame at the end where he looks like he's about to give into a monstrous side that he is never even mentioned having otherwise. My guess is that the scene's where he's with the gargoyles were initially him alone as his human and monster sides fought for dominance, maybe he even interacted with the arch deacon then, explaining the infrequency of his appearances in the movie.
But it is not just the Gargoyles that feel out of place, Captain Phoebes of the royal guard is a knight in shining armor who looks and acts like he belongs in a more typical Disney story than this dark tale of "black and grey" morality. He was in the original book, which I have not read, so I don't know how he fits in there, but the movie deviates a lot from what I've heard about the book and he is just in the wrong movie. It doesn't help his case that the movie could go on fine without him. He doesn't do anything that really helps drive the plot. The few things he does do could easily be done by others. The only purpose he seems to really serve is a love interest to Esmeralda.
Also, the movie felt like it should have had at least a bittersweet ending, if not a Pyrrhic victory or a downer. Instead we got a happy ending, but there was a moment where it looked like Esmeralda was dead and it felt like she should have stayed that way, instead it turns out she's alive and wakes up just in time to save Quasimodo, Frollo dies and they all live happily ever after (until the sequel).
Though there is one thing of interest; the last notes of the triumphant ending song are the tune of Hellfire, but in major key.