When you say that you 'don't care' and 'whatever makes for a better story is fine by me', you're being contradictory. If you don't care about retcons, it means you don't care about what was good so far. Indeed, when things are like this, nothing stops someone at the staff room from just having this great idea about how Anders and Morrigan, apostates extraordinaire, should join in the apocalypse and even become a couple. Boom, players can keep their silly headcanon and we move on with our lives.
In fact, you sound like a particularly bullshity biodrone from the BSN, who would keep repeating 'I don't know what you're talking about, BioWare's doing a great job to me because, so far, I made the right choices'.
Not sure how I am sounding like a Biodrone while talking at length about how I dislike what they're doing and fucking up, using the Witcher 2 as an example of doing it right, but... uh... okay.
As for your main point, I think the story should be best for the game it's actually in. I take games much more as single entities than a lot of people here I have noticed. I want X game to have a great story with a lot of choices, but I also want Y game to do that same for whatever possibly different reasons and narrative is necessary.
In other words if X game is enhanced by letting you wipe out Bob's Faction, that's great. And if Y game is enhanced by assuming Bob's Faction still exists, that's fine. Do what works best. If it's a planned out from the start series about the same character, like Mass Effect, then that changes things somewhat and you can probably carry stuff over. Dragon Age though? Do whatever makes Inquisition a better game, I care fuck all for whether I actually did the Morrigan ending or not if assuming it happened makes for a better game.
TL;DR As someone else hinted at it seems like Bioware are forcing the choices carrying over in the Dragon Age series because doing it in Mass Effect, which makes ten times more sense, has made it "their thing." I think that's dumb.