Initially, I was planning to end this story when Homura is reunited with Madoka. There would be the classic magical girl scenes in the beginning, and then the narrative in which the secret of the town would be revealed; that would drive the beginning and middle parts, and in the end there'd be the final showdown with Kyubey.
But I had a hard time deciding on the ending. Ending the story with Homura and Madoka being reunited wasn't really the best outcome. After all, the instant Homura encounters her, she'll be guided by the Law of Cycles, and disappear. Would that make her happy? It was also the director, Mr. Shinbo's opinion that the outcome of the TV series, "a human becoming a god" might be too heavy a fate for a girl in middle school to bear. Since that was the case, I decided to try to come up with a way to create a story in which Madoka could escape that outcome.
But I'd already ended this story once, so it was hard to figure out how to expand it. That was when Mr. Shinbo suggested, "How about a story with Homura confronting Madoka as an enemy?" I thought, if that's at all permissible, then I'd suddenly have all these options open to me, and that's how the current plot developed.
Now that I look back on it, I think it might have pushed the boundaries of the viewers' sense of morality. I'm sure there are people who view that as a "bad end," and there are probably also people who are more forgiving. I think it's an outcome that straddles that borderline. But people watch because they want to ponder whether the outcome is good or bad, so if they knew from the start that it was either a "happy end" or a "bad end", then there'd be no point in watching it in the first place. And if it's clearly a "bad end", then worse and worse things would occur, and if ten people saw it, all ten of them would be holding their heads in their hands. This film left enough room for interpretation, so it wasn't a "bad end". In that sense, I think it was the kind of film that allowed people to accept whichever outcome they liked — "happy" or "bad".