>>4004260>>4004261I think it would be cheap to have a clean and happy ending at this point.
Homura controls the universe in a sort of gilded birdcage, where all her friends live happy enough lives (maybe Mami's parents are even alive again), but she herself seems miserable. We know Homura is exceptionally strong-willed, but she's got to have a breaking point.
Madoka and the rest of the Quintet will age and grow apart. I doubt Homura will interfere with fate out of respect for each of the girls, but it would take a toll on her. Once they age to the point of death, Homura could roll back time, watching them relive the same lives over and over again, growing more and more tired as it happens.
This leaves three ways to break the status quo: Sayaka's memories of Madokami, Madoka remembering who she was, and Kyubey.
Perhaps Sayaka will be goaded into reminding Madoka about her past by Kyubey, bringing the Incubators back to power. Walpurigisnacht is supposed to return, so maybe the Incubators will opt to place each of the Quintet members into the moments of their highest despair.
In the end I expect Madoka will fade away and Homura will be a god of everything without purpose.
But what the fuck do I know. It'll have to be based on some literary work and I can't recall anything that would fit the plot.