FJH said: After countless timelines of having to put up with his Incubator nonsense, who is Homura still hanging out with in the post-Madoka timeline?
My idea of Incubator was always a more of a "cold, mechanical" type more than an "evil" type. He wasn't out for the destruction of anything - if anything his cause was noble in the long run. He just didn't have any understanding of human hardship or emotion. All he was doing was putting into motion a solution that was found for a much larger problem.
Madoka essentially made an "alternate" solution available, so, the post-Madoka timline Kyubey is fundamentally different - a machine with a different setting, if you will. I think Homura understands this, which is why she doesn't seem to mind him too much, even after everything that was done pre-Madoka.