Except Homura really wasn't a villain, even in Rebellion. Everyone was lured into a false sense of security after season 1 thinking that Madoka saved everyone. The problem is that despite how radical Madoka's wish was, it did not fix the root of the problem which was the incubators energy balance problems. The incubators were going to cause more suffering through Godoka until Homura "broke" the system with her witchifying. Even this is still a bandaid to the problem, but I was really surprised that the fanbase thought that Homura was wrong to stop the incubators. Perhaps if this was the case, the moral of Madoka is that compassion and equality can only be practiced with an abundance of resources and a lack of needs. Just as we eat animals (and plants for your vegetarians, just because a organism is not animated does not give it any "lesser" living value if you want to look at it from that perspective) for nutrients, the incubators harvested humans out of necessity to counter entropy. Dear Madoka, Kyuubey was actually the secret protagonist!

Except the "solution" the incubators came up with was to basically to burn the occasional (magical girl) soul to fuel a "fire" at the risk of possibly destroying the universe/existence. (Were Madoka/Homura the only magical girls to make a universe re-writing wish? Probably not, seeing as the side-stories sometimes didn't even mention the Walpurgis Night.)

It was a bullshit solution to a hypothetical problem that is so fatalistic (possibly no-win situation), its not even meant to be solved theoretically; its a philosophical question.

Agreed. Although I thought that the destruction of the girls served to decrease entropy, so would not that suppress the impending doom? I never even thought of the idea that the side girls could have had similar ambitions as Madoka. It would be mindblowing if the incubators witchifying was on a mind-fuck on the scale of purposely enticing girls to make such radical wishes in order to harness the anti-entropic powers of newly created universes. Goodness, you could get a Mirai Nikki kind of plot, where the ones in charge change universes like socks.

I'd have to check that, but it ultimately doesn't matter. Based on the main story's ending/the movie's ending combined with the manga/video game side stories, we can assume that its possible for other magical girls to make similar/ultimately universe re-writing wishes. (We're never told/shown those stories.)

By extension, we can also assume there are magical girls who chose/have already chosen to (ultimately) use their wishes to make the entropy WORSE. (A "I will be the last to have to fight"-magical girl wish would become "I will be the last to have to fight because there is/are no more universe(s) to fight to protect"-witch.)

Good job making it worse incubators!

I'm not sure thats right. It was a really bizarre set of circumstances that set up both of these wishes. The first one was set up from Madoka's karmic whatsit to ridiculous levels from all the resets Homura tried to accomplish, and from what I understand that was the only reason Madoka's wish power levels were over nine thousand and able to fundamentally screw with the universe like that

Homura's was equally screwed up. First off it wasn't even an incubator wish, it was her doing something to her soul gem that not even the incubators knew could happen. The lead up was all goofy from the incubators trying to isolate her from the cycle, and she was the only magical girl alive in existence at that point who even knew who Madoka was and would love her enough to try to keep her to herself like that, which is what turned her soul gem into a dark orb.

Of course theres always the chance that this current system was the basis of a wish based off an entirely different system in a past universe. Maybe the incubators harvested happiness energy instead and were cutesy because they were nice, till some bitch with hella karma decided to wish-screw the world