Regarding the open world:
Hinterlands was probably the worst area in the game imo.
Its too big, too aimless, takes too long to complete all the quests, and some of those quests are too high level to complete unless you come back later. I know you aren't supposed to do it all in one go, but that was a problem since most players of these games prefer to complete areas in one go rather than backtrack later.
Unfortunately its also the first area of the game, which I think soured a lot of people on the open world before they really gave it a shot. On the whole, I like the open world, it gives a sense of breadth to the areas and the world. I enjoy exploring. I like that each region is just a small part of the country its in rather than the Elder Scrolls approach (With major cities the size of small villages and entire countries being smaller than Rhode Island)
Regarding choice and consequence:
This is something Bioware clearly struggled with. They seem reluctant to invest resources in truly divergent content. I get why, but sometimes it just looks lazy, like the mages and Templars closing the Breach scenes being identical right down to the animations. They need to invest in a little more show and less tell.
This applies to the War Table missions especially. I enjoyed them, I felt they succeeded in making me feel like I was actually running the organization, but they felt sequestered from the rest of the game. There should have been more reactivity for some of the missions, such as opening up quests in the game world. The most egregious offender is the Clan Lavellan quest chain, where the Inquisitor's family and friends can get slaughtered without a single comment from the Inquisitor or anyone else. That needed a real reaction scene, full cutscene, or it simply shouldn't have been a War Table Mission.
Regarding story:
The weakest point for Inquisition for me was the story. There were individual elements I liked quite a lot: In Hushed Whispers and Champions of the Just were great. In Your Heart Shall Burn was a phenomenal introduction for Corypheus. I enjoyed Adamant Fortress and the Fade (Though I thought the overall plot of that questline relied too much on Grey Wardens holding the idiot ball). I even liked Wicked Eyes and Wicked Hearts. The Temple of Mythal was also well handled and interesting
As a whole though, it was a mess. Most of these storylines were far too compartmentalized. We were led to believe that the Mage-Templar War had the countryside in chaos throughout the south but (Apart from the admittedly well put together area with apostates and Templars fighting in the Hinterlands) it was entirely confined to one area and resolved all too cleanly very early in the plot. The Mage-Templar fallout should have been threaded through almost every area. Celene and Gaspard should have been trying to attract mages to their armies. There should have been various apostate groups, some staking out a fiefdom in Orlais or trying to hide, or resorting to blood magic. There should have been roaming bands of Templars looking for them, or maybe a Templar that takes advantage of the chaos to establish a little fiefdom with his own men, or even Templars that have abandoned chasing the mages altogether to protect a small village from demons. It didn't have to be in every region, but it shouldn't have become irrelevant before the game reached its halfway point.
I could say the same of the Orlesian Civil War, though my problem there is more that Wicked Eyes and Wicked Hearts needed much more buildup. We should have been introduced to Briala and possibly Gaspard beforehand, explored a plot regarding Briala's use of the Eluvians. Instead it was very self contained and it became hard to care about these characters when we arrive in Halamshiral.
Finally there's Corypheus. In Your Heart Shall Burn was a great introduction for him, but it was all downhill from there. After finding Skyhold he is defeated at every turn and his sense of threat dwindles to nothing. The Temple of Mythal was good, but by the time we got there he didn't feel very threatening as we had already thwarted most of his plans. The final battle was too abrupt, just felt silly and did nothing to help support the idea that he was a credible threat.
EDIT2: I feel I should say that Corypheus had great potential and I enjoyed his motivation, his loss of faith and his feeling of being out of his own time. That potential was just sorely underdeveloped.
Regarding tone:
After DA2, I understand that the developers felt pushed to play it safe and go with a save-the-world-storyline with a subverted chosen one trope. The problem is that they took it too far. This is a problem with many Bioware protagonists actually, but the Inquisitor was hit by a particular smothering barrage of ego stroking and constantly being told how special they are. Writers, stop. Your players don't need to be treated with kid gloves like an insecure child. I was thoroughly sick of it by the time I finished the game. I'm fervently hoping for a more grounded story in DA4.
Now, to move onto the tone of the world itself, what bothered me about DAI's world was that everything seemed designed to be "safe". And by "safe" I mean politically correct and going out of their way to avoid offending people. Even when it came to more controversial topics, like homosexuality they didn't just make Dorian gay, they also made him "the Good Tevinter". They didn't just make Krem transsexual, they made him as likable as possible, pleasant and also "a Good Tevinter". Generally they seemed to be trying very hard to portray acceptable characters. Even the NPCs in the world mostly consisted of well meaning individuals with relatively few taking advantage of the chaos for their own ends. In general, the way people easily set aside their own agendas to help the Inquisition seemed far too easy at times.
The only major exception to the above trend seems to be Sera, which might be why I like her so much.
EDIT: And possibly Viviene, she was well done, I respected her even if I didn't like her.