*Dean's Usual Well Written Stuff*
I feel a ramble coming on.
First, it's time travel. And not even 'time travel is the point of this story', which can be well written, but instead 'time travel as a random excuse'. That's never going to be good, and DA:I is even worse because the time travel isn't even consistent around the world. Oh no, it's just limited to some nebulous area around Redcliffe because they needed it to be. Frankly, in my opinion, they'd have been better off dumping the time travel aspect altogether and had someone from the Ferelden monarchy show up at IHQ with a request for the Inquisition to assist with a Tevinter problem in Redcliffe instead. The hellscape future could have been a Fade illusion due to all the magic being thrown around the Hinterlands or some such.
As for Fiona. I get what you're saying about the people who aren't aware of her characterization in the books having no reference to know Fiona is anything but some spineless loser who wilts away at her new master's slightest harsh word, and I agree there. And you are well aware of how I feel about the character of Fiona from the books. Honestly, she was written terribly there, too.
It's the jarring shift from writer's pet who can mouth off to anyone and who succeeds in spite of common sense or realistic storytelling in every instance to the 'you used a harsh tone with me so all my arguments are invalid' whiner in Redcliffe that begins to make me question the quality of the writing in this specific case. There's a consistency issue. You see it as the result of off camera hardship beating her down and so on, while I wonder why, since she's certainly never been self-aware enough to recognize when her ideas are bad before, she would suddenly (to our perception) start now? Why would she ever think or admit she could lose, since her go-to tactic is 'be a ****** and fail your way to success'?
To be clear, I'm not against the removal of her writer's pet status. I just think it could have been written in a way where she finally receives her long overdue failure while remaining consistent with her insane 'blindly stagger forward while being cocky/grating to the point of caricature, and damn the consequences to everyone else' characterization from the books. Instead of whimpering off into a corner the moment Alexius said a harsh word to her, I'd rather have had something like her continuing to mouth off to him until he grew bored with her insubordination and had her physically restrained or removed, preferably by other members of her rebellion who had been convinced to join his employ. In my mind, such a scene would have served several purposes at once; She would still have been the brash idiot from the books, there would have been direct demonstration that Alexius had people infiltrating the Mage Rebellion beyond a vague and easily missed reference (thus explaining a some other inconsistencies with the whole mage plotline), and it would have been a nice start to demonstrating that her immunity from negative consequences was a thing of the past.
That last is, unfortunately, something they never follow through on, which is just another example of how poor the writing is around the character. Surely the discovery that the Venatori had been murdering the Tranquil should have been important enough to reveal to the Mage Rebellion? Need something to judge her for? I'd say the fate of the Tranquil under her watch is more than reason enough to bring her up as unfit to lead, if not outright negligence. (As an aside, isn't it odd how, for all the whining about how Tranquility is evil and the cure is the greatest thing since Betty White, the mages were certainly quick to abandon the Tranquil and ignore their disappearance?) Surely Fiona's complete failure to safeguard anyone under her care should have been enough to at least cause the survivors to come to their senses and appoint someone else as their representative.
Long story short, I think it's poorly written not because Fiona has ever been well written, but because I feel the inconsistencies around her are simply too jarring, and, to me, their attempt at the character evolution you describe simply fell flat.