Hating an actor's performances and the actions of a character they play because they're a jerk in real life is silly. That shouldn't effect your opinion of the film itself. As for Shia in this movie, he was better, but like much of it I have no strong feelings one way or the other.
I don't really see what doesn't make sense by the way. I mean seriously, the second one's plot baffles me to this day (though I can tell you that it has nothing to do with enslaving humanity. The Fallen wanted to blow up the sun or something equally stupid). This one's was comprehensible. Characters had motivations, and it was actually explained, unlike anything in RotF. Hell, there were even some decent scenes of drama and plot-focus, such as the reveals and the really good pre-credits sequence, though those were dragged down by the pacing. RotF had none of those... And it was dragged down by the pacing.
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^Poorly disguised anti-caps sig