If you ask me, Bioware's "save transfers" do much worse to "invalidate" your choices than just choosing a canon. Many of the choices you make in ME and DAO are given a lot of weight and implied to have long-term repercussions on the world at hand. But since they can't actually do anything to make those repercussions be felt from game to game, they basically stuff them into a sloppy one-size-fits-all scenario where more or less the exact same things happen. In the end, cause-and-effect are rendered moot because of them.
What's the big difference between saving the Council in ME1, the highest government officials in the galaxy, who represent the three most powerful races, and letting them die to be replaced by a new Council that favors humanity? Watching a dopey cutscene where a Turian makes quotation marks with his fingers. That's
it. The Citadel still looks the same, it has the same (silly) security measures in place, run by the same people, and with the same anti-human politician running for office in Zakera Ward.
When a canon situation is chosen, it has a much better chance of
respecting causality.
Perhaps it's even better to not have any relation to the past game at all. Maybe some "easter eggs", I guess, that made certain nods to your past actions.
For example, instead of having a "canon" lore book of the dragonborn, have it reflect your choices. Dragon Age II did this. There's a lootable book about the Blight of DAO, and it's content changes a little depending on how your other character played through that game.
Dragon Age 2 also has a bad habit of outright ignoring many of your choices to do its own thing. Killed Leliana, Zevran, Justice, or Anders? Too bad, they all show up anyway.