I see a lot of people slamming Hydaelyn for not being more upfront about herself with the Warrior of Light, but it seems like that would've been a bad idea.
Imagine that A Realm Reborn starts with Hydaelyn introducing herself as a Primal, and mentioning that she wants you to defeat the other Primals on the Source to help save Eorzea. And then you get to Ifrit and find out that Primals brainwash their followers into following their will, which usually puts them into conflict with other gods (as we see with Garuda fighting against Titan and Ifrit later). What's Hydaelyn supposed to do to gain the Warrior of Light's trust at that point? Would the fanbase really accept the answer "Nah, you're not brainwashed. I'm actually a good Primal!"?
I don't really understand why there's a portion of the fanbase that wanted Hydaelyn to be evil anyway. Even from the beginning of the story, other Primals like Ramuh offer sentiments about Hydaelyn that suggest that she has good intentions for the world. We don't get the full story and she's secretive, sure, but I never got the impression that she was being intentionally malicious. Heck, the biggest anti-Hydaelyn speakers were either the crazy, evil Primals or Lahabrea going on about how much he wants to destroy the world and let chaos reign!
I think they're referring to how Hydaelyn's backup plan would be for the people of Etheirys to flee elsewhere, which would lead to Meteion destroying the world and thereby the other reflections of Etheirys. Thancred, notably, was not entertaining the possibility of not fighting Meteion because he was worried about Ryne.
That said, if Hydaelyn is tapped out on power and the Warrior of Light can't defeat Meteion, I'm not really sure what else the backup plan could be. It's clear Hydaelyn would prefer that they can defeat Meteion, but she left an out for the people of the Source so that SOMETHING could survive in the event that result wasn't possible.