The problem I have with your edit is this: People are already complaining about how empty some of these areas are. While I question the logic of the Hissing Wastes being packed with mobs, all things considered, delegating the clearing of what's there to NPCs with no real involvement from the PC relegates the game to more of a Roller Coaster Tycoon situation, where all you're doing is RTS type stuff, instead of actually developing your character. That's not what I signed up for. There are missions where you can send out the troops to deal with stuff, some of the wyvern quests for example in the Western Approach, I think... However, even if we were limited to "closing rifts", we still have to travel to those rifts. They aren't "teleport to this one, then that one, then that one", in that we have to travel to them, and having the terrain be devoid of any life whatsoever doesn't make for interesting game play; again, see the complaints about the Hissing Wastes.
My issue is that it doesn't immerse or make sense to me how zones, rifts and keeps were handled in DAI compared to what could have been done.
For example if DAI was real life, a movie or a novel, do you think the Inquisitor as a figure would be taking keeps/rifts solo with 3 companions? Do you think the advisors or the Inquisition as whole would even allow for that?
No. In an immersive sensible plot the Inquisitor wouldn't have left Skyhold without hundreds or even thousands of troops close behind after "In your Heart shall Burn." Rifts would have been taken care of mostly through troops fighting off hoards of enemies with the Inquisitor safetly approaching to close Rifts or take keeps once they're secure. Doesn't make sense to have someone who's so important to the worlds future doing 90% of the leg work in all zones with three people. The Inquisitor getting killed by some stray arrow would have literally meant the end of the world.
Also the Inquisitor wouldn't have been doing many of the non-combat side quests they were doing. I thought Hinterlands was a good start for the Herald to prove they're an "agent of the people" in a starter zone (gaining initial power and influence), but the leader role became less evident over the course of explorable maps not more.
Now we can't have the Inquisitor do nothing though since it is a game and player agency is needed. 
The way I would have done it (posted similar things in other threads) is design everything main quest-like and epic through and through.
Rift closing? Each one would have been a hassle with hoards of demons and with many more involving Crestwood plots like the underwater Rift. I have floated a Battle of Denerim mechanic a few times where you call Inquisition forces based on camps controlled in the map to help take keeps/rifts. You can choose not to but the fights would be very very demanding. Super Rifts such as these would have allowed for more "world ending" design and feeling across all zones.
Keeps? Same thing. More numerous and challenging foes involving the Inquisitor and his troops. Battle of Denerim-like mechanics again and the option to send ravens back to Skyhold, requesting advisor support (like siege weapons, basically reverse war table). The ravens may have even been a means to start the quest, with Adamant-like cutscenes and a siege. Dialogue, speeches, decisions and cutscenes with troops could have been used as well to define how your Inquisitor leads in Battle.
Settlements? A while ago I thought up an idea of having settlements on explorable maps where you claimed them. Once claimed it triggers cutscenes where the Inquisitor would demand an audience with the town's mayor or its people to hear their petitions or problems. How the Inquisitor speaks, responds and sounds triggers different side quests and war table operations. Completing these would give the Inquisition control over the town, more power and influence and more troops to use in the reinforcements mechanic.
War Table Operations? Little cutscenes with the Inquisitor making an appearance (with dialogue) in some would have been nice. Going to the Haven memorial after finishing the operation to make a speech being an example.
As it was, there was no development of character for the Inquisitor in many of the side quests, maps and war table operations. The quests were too small and underdeveloped for the protagonist's place in the world.
I don't think people would have cared about player agency if it was done as above. The cool factor (well I think its cool) would have been enough and fitting. Remember the leaked pre-alpha video that showed us an early Crestwood where you have to decide the fate of Crestwood or the Keep? A lot of people were hyped for DAI based on that one video. It probably was cut early on, along with customizable keeps later, because they were going to take too much development time and resources. But I can dream. The Witcher 3 vs. DAI side quest debate would have bee much more interesting though that's for sure.
It's unfortunate because I doubt the DA team will get another opportunity because it's most likely passed with DAI. Unless we get another messianic leader of a continent spanning para-military force or a royal/general leading his/her country
@Ghostbusters101: I 100% agree and was where I wanted to go with my post. I think a lot of people think they like total customization because of various reasons (like nostalgia of older D&D games like BG/IWD/Torment), but in reality they never take advantage of it (as data suggests) and they would be a lot more happy with RPGs that have totally pre-defined characters. Ones that fit their usual pick (Human Male Solder/Warrior archetype). I just hope Bioware keeps making their games better based on customization rather than making a copycat of Witcher 3 because of loud demands to do so. 