1: The MLP movie is gonna be the "real deal", so I can see it going over 100 minutes.
2: The movie is most likely gonna be 2D only. I don't know how they could do 3D all of a sudden.
3: Probably a G rating, but a PG rating is still possible. Like you said, having a PG rating can give the writers more freedom for a darker story.
4: It's hard to say. Besides haters, the show seems to be getting decent reviews at least. In terms of the brony community, unless the staff really screws up the movie somehow, I can't see the community hating it. In terms of box office success, that's gonna be a bit hard, because I already see a few movies that are definitely gonna be popular next year. The show is definitely popular, but I think Hasbro still needs to advertise the movie a lot, otherwise it'll get overshadowed.