A reconstruction doesn't have to simultaneously deconstruct the trope. That's why I cited Toppa Toppa Gurren Lagan as illustrative of this type of approach.
As to the merits of DA:I, I don't see why a heavy focus on an antagonist is particularly necessary. Ignoring the fact that DA:I is the only game Bioware's had besides ME3 that actually coherently ties the majority of its main quest to the antagonist, the Elder One is pretty clearly written to be the antithesis of the Inquisitor. I thought that this was so on the nose in the writing that it was one of the biggest weaknesses in the game. As for what DA:I addresses that's both a deconstruction and reconstruction with Corypheus, well, there's a big one. Repeatedly losing as an antagonist actually saps Corypheus's strength. Unlike every fantasy villain since Sauron, he's not a load bearing boss. This concept is stupid and Bioware uses it again and again pre-DAI. The best examples are Sovereign/Saren and the Archdemon.
To have the villain lose in a way that's actually realistic - slowly being whittled down to nothing - is ambitious. And it's led to a great deal of hate specifically because it's not the usual nonsensical encounter where the enemy has an overwhelming force and then just gives up and runs away when the load bearing boss loses.
I'd like to say that while I disagree withyour conclusion- about why Corypheus is derided- I totally give you props for the analysis and assessment on the context.
For me, Corypheus's issue wasn't so much a gradual whittiling away of his power base, as much as a lack of credibility in that power base after Haven. Part of the cost of having the three main post-Haven quests be build along the lines of 'we must foil Corypheus's plan to take over Orlais/seize the Wardens/find the Fountain and reach his victory condition' is that, well, by foiling him we kept him from having that demonstrated and credible power base that truly threatened us. And considering that Haven wiped out a significant part of the Mages/Templars that he recruited instead of us, the rest of it was kind of... out there. Told, not shown.
Don't get me wrong- I love the Lion whatever it was in Orlais, the area where there was an honest-to-god Red Templar strong hold and Corypheus bastion. That was an excellent example of the Inquisition chipping apart Corypheus's support base- but it was also entirely optional, and had no impact on the plot. All the non-critical exploration zones were, and that's a shame because that's where the 'we're fighting back-and-forth with Corypheus' was best. You didn't have to fight through these things to get to Corypheus, so the power base we did see was mostly irrelevant.
I think Corypheus was undermined by the structure of the plot, and the linear plot of the critical path was undermined by the open-world filled with utterly irrelevant optional areas. Because of that, the vast majority of Corypheus's agents and influence are just kind of... irrelevant.
One solution would have been to make the regional quests sorta-mandatory in order to access the next part of the crit path. Not by the Forces mechanic, in which scavenging a couple rocks or herbs was enough- but tying the regional narratives into enabling the overarching plot. Make us solve the local problems to have the support to solve the bigger ones, rather than just picking up rocks.
So, for example: pre-Mage/Templars, we have to get to Orlais to confront the Chantry. In canon the game gives us a benchmark of Power we have to accumulate, and to get to the suggested level you need to go to the areas until you kill enough things and do enough quests to level up.
But why not make part of the first areas a question of 'how do we get to Orlais from Ferelden'? Going north to the sword coast is about trying to secure a port of sorts that you could get a boat to take you to the capital. Or you can go south, where the Inquisition soldiers in the marshes were looking for a better path through/around the Frostback Mountains, and that path allows you to get to Orlais as well.
Then, post-Corypheus, when we have to get to Orlais: why not make the war zone and the Freemen of the Dales mandatory things to get our foot in the door? Say that we have to do one or the other in order to get an invitation from one of the actors: rescuing/contact the Duke's men in the war zone gets you the Duke's invitation, while Floriana will invite you on Celene's behalf if you wipe out the secessionist Freemen of the Dales who are giving Celene headaches down South.
And for the Temple of Mythal, why can we go straight there rather than have to do some elven archeological treasure hunts to find clues on its location, a sort of race-against-time against Corypheus's own agents doing the same? Fighting Venatori in the wastes could have been a lead into the Grey Wardens plotline by pulling the Venatori conspiracy angle. Liberating Empress de Lions from the Red Templars could have provided vital intel on the Red Templar marching orders and freeing up the Orlesians to send their forces against the Temple of Mythal. And all of these could have been required before even being able to get to the Temple of Mythal, rather than the arbitrary power count.
Tying the regions into the plot, making the Corypheus presence in them a vital part of his operation rather than negligable, wouldn't have just helped the story structure- it would have helped make Corypheus a more credible actor because he forces would have been in the field against us trying to stop us. Not just... 'oh, we don't know where he's hiding, but he's got armies and ****.'
Then, at least, Corypheus's last-ditch effort might have made a bit of sense for a climax... even if the setup of that climax was itself anti-climatic in the extreme.