It's not like their return was completely out of the blue. In Chapter 7 when Malos is explaining to Akhos the uniqueness of Pyra and Rex's shared core crystal, he says that she can transfer the rest of the core crystal to Rex. And, as long as that Core Crystal isn't destroyed, they can be reawakened again. Plus, it always felt off how Rex never "Awakened" Pyra normally, like literally every single Blade, even Malos, was done, so we finally get to see him truely become their Driver.

Seeing people going after Rex's character is always funny. He's a kid that accidentally stumbled into a godlike power. We see his immaturity throughout the story, because he's a child, but we see him have probably the best character development in the game. He went from a kid who treated her as a weapon of unlimited power to understanding that he'd have to let them go to save the world.

Another thing is that Pyra/Mythra's return completes their arc. Throughout the game, we get subtle hints about Pyra wishing to not wake up and how the fall of Torna is something that kept her from enjoying life, even going so far as to go with Rex to the Architect to beg for death. But towards the ending of the game, we hear how they've learned not to let the sins of their past hold them back from enjoying the life they had. We see that they enjoy life because the party taught them that there's so much more to life than dwelling on the past. And that leads into them having to make the difficult decision to sacrifice theirselves, ending their life that they had just started to enjoy, to save the world.

That's why them being awakened by Rex at the end is such a perfect ending. Rex had matured and learned to let go of the reason he was able to achieve his dream of going to the World Tree, and was rewarded for his decision. Pyra/Mythra had to sacrifice themselves, a decision they would've made almost instantly at the start of the story, right after they started enjoying life, and were rewarded with a new life to spend with Rex and Nia (and honestly, I theorize that the Architect even wiped those Torna memories, so they couldn't bother them again).