One thing in Bioware games (at least in recent games) is that it does feel like companions are untouchable. I liked what they did with the sequence of Hawke and Stroud, that actually felt bold in terms of writing. However, the actual group companions seem as if Bioware never wants to touch them with a ten-foot pole. There's so much drama to be had if they would be willing to "kill their darlings," or at least maim them. I'm not sadistic, I swear! 
Anyway, I think the main thing I was disappointed about was that it felt like Skyhold was never in danger. Granted, the Inquisitor makes short work of Cory's army, but how epic would it have been to have a big assault on your keep? It didn't even have to be Cory; it could have been his dragon and the last remnants of the red templars assaulting. And then you have to go back to the site of Haven and the breach to face Cory.
I understand why they didn't do that, seeing how the dragon was directly linked to Cory and such. But, it would have been pretty neat. And maybe it wouldn't have felt less anti-climatic to some. To me, the ending wasn't terrible. It's obvious more is planned either through DLC or a next game. It had it's resolution with the main villain Cory and set up a few elements to hold onto for whatever is next.
Maybe people don't like happy endings because of the influx of tragic endings flooding games nowadays? They're not used to seeing them as often and such endings possibly feel incomplete or out of place. I will admit that the ending of DA:I felt so....wrapped up that I didn't know if I should feel satisfied or not. But, thinking about it, the main story was completed and the rest felt like stepping stones into something bigger (especially that post credits scene). I loved my Inquisitor, adored my companions, and felt like a badass. DA:I managed to make me feel like my Inquisitor and advisers weren't just for show, that we meant business and were going to get results. And we did. That was the goal.
Also, I think that Inquisition was to show that Cory, even with ripping a hole in the sky, was only a small part in the grand scheme of things. He's a small fish compared to the big. There's much more than meets the eye.
With all that said, I do understand the gripes people have with the ending. Even if I didn't mind it, there is plenty to critique.