I thought the story was delightful. I never really felt like nothing was going on and I felt like the threads between the main events were very clear. I also didn't feel like the ending was any kind of "cliffhanger" - that would have been if the story ended with Hawke and Meredith leaping at each other and "TO BE CONTINUED IN DRAGON AGE 3 OR EXPANSION LOL" came up.
I did feel like O's betrayal was a bit arbitrary - we basically completely slaughtered a few waves of Templar (surprise, rushing a bunch of mages through a tiny hallway is a bad idea) and then he panicked and Went Insane. If there had been any kind of imminent danger I could have seen it, but as it is it didn't quite work for me. I ended up just putting it down to pressure.
While I'm complaining, I think my biggest story-related complaint is the dialogue wheel in really important plot moments. To pick an example that stood out to me, Varric and I have just managed to subdue Bartrand and I'm telling him what I think he should do. My choices are like... "let him go" and "kill him." Okay, kill him is pretty unambiguous, but what about let him go? Is this "don't kill him, Aveline can find him a nice quiet cell and we can try to fix him" or is it "I'm stupid and routinely make poor decisions that get other people killed, so let's let him free in the streets of Kirkwall - what could go wrong?"
I decided to take the chance and it turned out it was the former, but I really would have liked to know that at the time. There were other places in the game that I felt the same way. A lot of the time the dialogue wheel worked really well and I enjoyed seeing how Hawke would play out the line, but at those critical points I felt its detail was lacking.
Maybe what I liked about the story and ending is more helpful than what I didn't, though. I felt like the buildup was really good and I enjoyed having a slightly more down to earth story without some looming, impractically-sized villain. At the same time, the plot followed logically from one point to the next. I liked seeing the characters recur between the years - Thrask, in particular, I always looked for and clicked.
That said, I did feel like there wasn't enough sense of time passing between the acts. At any of the intermissions Varric could have said "then, one week later" instead of "three years later" and I'd have been none the wiser. The same merchants were standing in the same spot hawking the same wares. I think more attention to detail there would have gone a long way.
Actually, if I could have another complaint it would be party size. I felt like the party was a little small to get everyone I wanted in it. I didn't feel like I could comfortably drop Anders in some of the fights because of Merrill having no healing (this being a big deal in the High Dragon fight in particular, IME) and that led to me excluding Varric even though he was my favourite character. That made me sad! I guess I could have just put it on "super easy", but then the combat would have been less fun the rest of the time.
It's also worth noting that I did like being able to have my ending where everyone ended up, if not BFFs, at least alive and together (other than the part where they part ways after the end, I mean). Dark fantasy is all very well but at the end of the day I like the ending to be happy enough, and the everyone standing together was great.
Anyway, I'm sorry for blabbing on so much. I don't have a Bioware fangirl club card or anything but I have bought lots of the games over the years and I really wanted to say something positive against the sea of metacritics and other assorted nonsense. I hope you won't let it get you down and am looking forwards to the next game.