I hated how you had to fight both the first enchanter and the knight-commander no matter what side you supported. All your support doesnt matter. Nothing changes.
Another thing that pissed me off... After I beat it, I loaded to just before I helped Anders by distracting the grand cleric. This time I told him to fuck off. The chantry still blows up and they both act like had helped him.
The only real change you can make to the game is with your sibling and whether or not you kill Anders at the end.