DAO gave you a meaningful choice of how to end your story, including a few rather nice outcomes for the Warden. I don't think giving us that choice adversely affected the story. At all. That they retconned some of that later had nothing to do with making a better story, but to start later games with fewer variables.
Inquisition with trespasser was an overall good experience for me,the loss of an harm and the anchor related to it, or of an organization who already absolved its task isn't a problem but a good closure,especially because these losses are not by accident(ME3) but tightly correlated to the story .
-The losses of the anchor is well orchestrated,it is basically an ancient elven key artifact of whom the character isn't fully capable to understand,the arm was exposed to it after a ritual incomplete and the situation got degenerated after some years,Solas himself was probably not capable to do anything for the Inquisitor during the main game (before that the arm was irremediable damaged)due to lack of power.
Plus the anchor wasn't yours it belonged to the wolf.
-The Inquisition disbanded and dissolved as an indipendent organization was well orchestrated and it's pretty realistic.
You cannot honestly beleive that a military organization which already absolved the task of which it was formed in the first place,will continue to grow like a cancer into the territory of two sovereignity nations without encounter heavy resistance while the others nobles will glance happily without doing nothing.
The Inquisitor absolved the task and now is free to continue to pursue Solas by others means and possibly under the authority of the Divine not as an indipendent and unwelcomed organization in sovereignity territory.
As for the whole DAO meaningful choices/outcomes i'm firmily of the opinion that even if those choices helped DAO and it's narrative as well as it's replayability value,those choices felt boiled down in the overall experience of the franchisee because they were often retconned or artificially negated to put the story in the predefined trail.
Take the Warden choice,does it makes a substantial difference to have Loghain/Alistair/Stroud? No is the same thing
Does it make a difference to have the warden dead or not? No it's the same thing,while you can argue that there is a difference in DAO,this difference is pretty much non existent in DAI,since that the character is basically a non factor even if the story took place in their home surf.
Does it make a substantial difference to have saved the essence of the final boss of DAO? NO because even if that choice seemed important beyond to just define your character in that moment,it was basically resolved into a meaningless smokescreen,little family comedy/drama,just to force the story on a path that you didn't chose in the keep.
So no i'm all against the DAO illusion of choices,not because they are an illusion (is always like that in Bioware games) but because sometime they do have the feeling to be earth shattering decision,while in truth they aren't meant to impact the story of the franchise and they are destinated to be resolved/ignored to allineate the story to the writers path.