@@Nightmare Muffin, What I meant by saying it wasn't her fault was that she had no control over her situation. I don't remember where this happened, but principal Cinch told her not to talk to the canterlot high girls. If this happened before she talked to flutters then I see her justified in running because Cinch held her future hostage. I will admit there were times I thought she should just say "Why are you glowing" or something like that, but I felt she never had the mental state required to stop ask such a question, what with the future hostage thing, and the games. That was a really stressful time. For both Sunset and Twilight. If Sunset was willing to talk and listen the movie would have also ended clean and quick, but she was stressed that pony twi was not responding. Taking it out on SciTwi.
And the question on whether or not twi should be forgiven is really a subjective one, and belongs to the characters. However, there is one objective reason that is important. The characters wouldn't realize this, but forgiving her and letting her stay would be the healthiest thing for Twi. She would be less likely to go all power crazy again because she has people she cares about and wouldn't want to risk hurting them. If the situation arose that she needed to transform we would now see a similar transformation to the one Sunset had when she saved Twi.
What would we get if the Shadowbolts were more fleshed out? compared to humane 6 they didn't do much more than them, And we already know so they seem more fleshed out. If we watched this movie with no knowledge of either school then neither would get that much characterization. If they made another movie with the Shadowbolts I'm sure that they would get more screen time.
I don't think it was a bad movie or plot. it may not have been the best movie out there, but it wasn't bad. All the reasons you wrote are outweighed by the enjoyable-ness of the movie.