I loved the story and the ending too. My spidey sense has always told me that war was on the horizon between the mages and the Chantry ever since DA:O! Of particular interest at the end was the fact that the Warden AND the Champion vanished. There's something bigger going on than just the Blight or the mage rebellion. I'm still trying to figure out what Cassandra and Leliana's Plan B is and what their goals are now. I also wonder who those "allies" that Nathaniel mentioned were.
Sorry to be scattershot, but I stayed up until 4AM (I think) to finish the game. I found that there were some surprisingly emotional moments throughout the story, such as Leandra's death. My heart sank when I saw that that insane bastard necromantic serial killer had her, but the Anders romance in particular was sheer torture. I felt betrayed and angry, but my Hawkette still loved him. Ugh, I just knew it was coming too after the potion quest. The salt peter reference with the sela petra made me think "uh-oh...BOMB!!!" Later, when the Chantry was destroyed, It was heartbreaking, especially after I saw Sebastian's reaction (I felt badly for him). I'd always thought Elthina was a genuinely nice person. She knew mama Hawke & the Amells...it was just a horrible experience. Still, as a mage, I couldn't stand what Meredith's oppressive rule and my Hawkette still loved Anders, so she couldn't off him even for doing something so horrible. I do sort of dread future events because Sebastian vowed to come back with an army, and he clearly wants Anders' head on a plate at this point (whether or not he finds Hawkette and Anders again is another matter though). I would really like to see an expansion.
I think the best way I can describe the emotional impact of the ending (from the Chantry explosion on) was similar to when my Warden got dumped by Alistair for being an elven mage and his later admission that he'd been a fool and sacrificed himself to save her. It was hearbreaking and painful but quite brilliant in terms of the story and characters.
Speaking of old characters, it was pretty awesome to see Leliana (in her new role), along with Zevran and Alistair. I got to see King Alistair, and the snarky banter was priceless (including his mentioning the old ball & chain, aka my Warden

- this was my rogue Cousalnd import I believe). Even the little touches like that note written by Avernus was intriguing. I think there's a lot of foreshadowing about future events if you're paying attention to things.