Here's a plot point that really threw me: the well of sorrows, why the hell couldn't I destroy it. I mean I get that there's the option there for you or Morrigan to take a drink, but man that really pissed me off since all the dialogue choices up to that point from my character were leading up to me letting the elf guy destroy it to protect the world. Then Morrigan just stabs that guy. I felt like my character (who I mostly played as a nonbeliever with a slight mistrust for magic) would have never let that slide and then I'm left with the choice of me taking the power or her. Also, I didn't understand what the point of turning the mage lady sidekick against Cory. All it did was let me avoid a fight, I was hoping for some in fighting among the ranks.
All in all I liked the character moments way more than the story. Blackwall, Dorian, and Ironbull all had amazing moments tied to their missions.