As someone else pointed out, 'retcon' is not correct term for what happened to TIM. He went the route of Sarek from ME1, wherein the Reapers dominate him through his fear and ambition. You might think it was cheesy or cheap, but what happened to TIM and Cerberus wasn't undoing what they previously were.
As for Morrigan, I remind you that Bioware people have said they see DA games more as the stories of Thedas -- not wed to any one character. ME has, thus far, always been Shepard's story. I won't say the OP's fears won't come to pass, but I think Bioware knows better and it's playing the long game with DA. So I don't think Bioware will 'use up' Morrigan and Flemeth in one game. The characters provide intrigue and continuity between games.
My (wishful) thinking, then, is that DA3 will:
-- Link DA:O and DA2 by connecting Morrigan/Flemeth's plans with the mage rebellion. I think you do so by framing the chaos as a symptom of the Old Gods' resurgence.
-- Have the player choose between facilitating the reawakening of the Old Gods or trying to exterminate them. I think the game would be wise to focus only on one Old God, saving the others for future games and milking the mage rebellion more. Regarding the OGB, I think there are lots of ways to work around the player's choice in DA:O to reintroduce Urthemiel (the Old God tainted in the Fifth Blight). This is a player choice I'm comfortable with working around, because the OGB has such rich potential and, honestly, there's a lot of uncertainty about what has happened to the Old Gods, whether slain or dormant.
-- Leave the player with a sense that he or she has had a significant but not definitive influence on the mage rebellion. I think DA3 will be more compelling if it ends with the protagonist feeling vulnerable during the violent birth of a new world order. More bluntly, DA3 should not have us play a messiah.
-- Step away from Warden and Hawke without remorse, and focus on the new protagonist's choices more than acknowledging those of old ones'. The Warden and Hawke have to be acknowledged, but I think DA as a setting (and franchise) will be best served by telling new stories, not reliving old ones. My basis for this recommendation comes from the unsatisfying ending to ME, and the realization that, the more choices for which a sequel has to account, the less meaningful each one seems. ME3 was a superb game overall, but it shouldn't be a template for DA3. It should provide as many new and compelling choices as possible. More than being comfortable with DA3 stepping away from DA:O and DA2, I feel it's a great necessity.
So, to reiterate, I'm optimistic Bioware won't resort to the cheap, disappointing storytelling the OP fears. As I've tried to suggest, there's too much rich storytelling (and too many more games) at stake to make Morrigan and the OGB into cheap, obvious villains. DA:O and DA2 did a good job of presenting compelling yet morally ambiguous characters and choices. Hopefully Bioware has the sense to stay that course.