The first time I watched Rebellion, when it had its limited theatrical run in the US, I really enjoyed the movie but I thought it was kind of counterproductive to the themes of the anime.
Having finished it again just now with a fresh analysis and renewed love for the original anime series, I have even more complicated feelings about it.
I appreciate its observations on the curse of knowledge that was touched upon in the anime. Knowledge is isolating. Homura's Isolation Chamber is a literal manifestation of that. There's imagery of the forbidden fruit.
But I can't help that its narrative feels like it meanders between several different ideas, unsure of what overarching statement it wants to make, and ultimately ends up in a scenario where it is forced to negate the meaning of the anime's ending. It's as if the very hope the anime conveyed succumbed to nihilism. It seems ill placed as a conclusion to the main story.
There's a lot to be said about Homura's selfishness in bringing about a world where hope again doesn't exist, and instead we simply forget the horrible reality of the world they lived in. Homura takes the burden of hope away and instead shoulders the responsibility of despair on the Incubators. It's basically a revenge fantasy. I think in isolation the narrative of the movie does come together. But it ultimately doesn't quite feel right in context.
When I first watched Rebellion, I accepted that I would take the anime's ending as the true ending, but enjoy Rebellion's narrative by itself. Even having matured as a person since then, and coming to appreciate the anime all the more, I think this second watch has reinforced my thoughts on Rebellion. Which comes as a bit of a bittersweet disappointment.