I think what especially infuriates me about Isseya, is that she COULD be a convincing antagonist in Veilguard, that would reintroduce a level of moral complexity into the game's structure and give you an interesting choice, without fundamentally changing much about the structure of Davrin's companion quests, and it wouldn't destroy her character and make her completely opposed to her initial goals???
In The Last Flight, Isseya hid the griffon eggs away because she did not believe the Wardens of the Exalted Age were appropriate caretakers of this sacred bond and burden. I think she should essentially make the same claims about the Wardens of the Dragon Age: after the events of the Fifth Blight, choices made by the HoF regarding Avernus, and then regarding the Architect/Mother, and then of course, the whole supporting Corypheus thing—Isseya does not believe that the Wardens of the Dragon Age are ready to handle the griffons. I think she ought to kidnap the griffon clutch and kill the griffon caretakers, in an attempt to put them back to sleep, and hide them until a future age where the Wardens will treat them better, so that they specifically WON'T be tainted by the Blight spreading through the world.
Davrin would still be determined to pursue this mysterious woman who'd killed his comrades and kidnapped all-but-one griffon, they'd still run to The Cauldron and find out both about Isseya, and the First Warden's attempt to try and taint the griffons and have sympathy for her actions—and then Davrin and Rook would be left with a genuinely compelling moral choice: do you agree with Isseya's decision and leave the griffons in stasis under her care, or do you fight her and free them, because you trust the Wardens/need them now?
Within the canon of Veilguard, the Grey Wardens are ruled by superiors whose first instinct is to neglect and ignore world-ending threats because of selfish politics. Although there are good Wardens like Davrin, Antoine and Evka, do you trust the institution of the Grey Wardens to properly treasure the lives of the griffons? Because you can't just limit the griffons to "good" Wardens—once they are out in the world, they will become the companions and weapons of Wardens you dislike! And in this age of horrible Blight, where things have gone to absolute shit: do you push to try and bring the griffons into the world anyway, because you need every advantage you can get to save the world? And I think this makes Davrin's personal storyline more about him, while still also being about the griffons! What does Davrin feel about this whole story? Isseya specifically protected the griffons from being discovered by anybody other than elvish Wardens—how does his feelings about being Dalish and being a Warden collide here? How do her pleas for protecting and preserving the past and keeping it safe from corruption and danger feel to him? Is he the sort of person who wants to protect the griffons, how does he feel about the Grey Wardens as an institution with knowledge of what was done in the past, what is he willing to sacrifice to save the world?
There's such room to make her an antagonist of Rook and Davrin without diluting her principles and morals, and without going 'The Blight made her craaaazzyyyyy and completely lose her morality!' but it would require the developers to allow players to explore and examine greyer moralities about sacrifice and protection and what we owe to the people around us, and offer us more than just blatant choices between cartoonish evil and naive goodness.