Things I liked
The nuances of faith - This day and age, religious faith is treated as quaint and little more than a vehicle to promote atheism. But Cassandra, Leliana, and Cullen did a great job of expressing themselves in a realistic manner.
The lore - It took Descent to do it for the dwarves, but I really liked seeing how the ancient world used to be.
The villainous sub-boss brigade - I got a rise out of them. I wanted to kill Florianne, and I thought most of the villains like Alexius, Samson, and Calpernia were very nuanced. And the ones that were unrepentant jerks, Denam and Erimond, were satisfying to kill. That's important for a villain.
The graphics - Thedas was vibrant and beautiful. Most games are just crap-colored brown. Thedas felt lush and real. The Bastion of the Pure and many of the open worlds were quite lovely
Most of the NPCs - The advisors were welcome, and Josephine slipped in easily. Her lack of military training brought a new vibe to contrast with soldierly Cullen and spymaster Leliana. Bull brought a nice clever hedonism, Cole was strange and thought-inducing, Solas (pre-Trespasser) was thoughtful, Vivienne was graceful and had a lot of nuance beyond her persona. Even Sera brought some crude humor. Almost all of them worked.
Things I disliked (not counting things like the beige pajamas, which were fixed)
BioWARE Nudging - I don't like it when the game pressures me to take choices that I don't want to take, and guilt-shames me when I don't (I'm an unapologetic Wrex killer because the story is better without him, and I hate how I'm constantly told how much worse things are with Wrex dead). And in Inquisition, BioWARE was definitely trying to get you to do In Hushed Whispers over Champions of the Just. No effort was made to even attempt to convince me to go to Therinfall, no extra scenes with Barris or some other sympathetic templar voices. They didn't even point out the realistic version: That the Breach, a hole in the Fade, would be reinforced by templars doing their thing, pushing the Fade back.
Moral choices aren't difficult - Even with the prospect of alliance, I can see no reason to join with the qunari: They've proven never to be trustworthy. I also don't see a reason to disband the Seekers, the problem was Lucius, and Cassandra already made a sensible plan. When two sides aren't presented with logical reasons for both, then there's no reason to make it a choice. Take my favorite DLC of all: Overlord. As horrible as it was, avoiding a war with the geth makes logical sense, even if you have to sacrifice innocent David Archer. I didn't get that with these.
Repeat fetch quests - I can understand killing some templars and bringing the wedding ring they stole after the (censored) killed an innocent man unapologetically. But when I have to go kill a wyvern and bring the liver back. kill a mage and get his key to open a shack, kill a demon and bring a Dalish's belongings back to his sister, it gets repetitive. I can understand clearing out a cave of crazy mages to help some apostates. But when I'm clearing out a cave of demons, a cave of spiders, a camp of templars, the ramparts of undead, a cave of smugglers...you see where this is going. The quests need to have a bit more variety, give more than just XP, and have some more banter with my companions to at least give them different flavor. Emotional resonance is good. Unabashed humor is also good.
SJW's unite! - Video games are not a good place for morality plays, particularly ones where you routinely slaughter people and animals for money. In a game when you can seize assets with a crazy law, let an Empress die, and where personal strife, be it racial, societal or whatever is common and treated as justified, it's so weird that we need to be utterly politically correct. You can't condemn Dorian for his ridiculous behavior, you have to be completely supportive of Krem, and other nonsense. This actually turned Dorian into my least favorite BioWARE, beating out Mary Sue's like Liara, Omega's Aria, and other bad folks like Eldath or Shar-Teel.
Enforced Irrelevant choices - This plays off the last one, and a few of the others too. You can railroad a plot if it needs to work a specific way (for example, you can't join Corypheus because the game would end, and you can't refuse to join the Inquisition because the game ends), but if it doesn't matter, don't force a choice the player has a high possibility of not liking. Conversely, don't give me a choice of how to feel if it's just three shades of the same thing. I didn't like Liara, but I was forced to be her friend and it really wouldn't have mattered if she was my enemy. Giving an ignore option is nice, but not enough.