The fact that Pyra/Mythra we're split at the end of XC2 pretty much guaranteed a direct sequel. To be complete, they need to become one person again. That was always my theory even before XC3 was rumored.
And now XC3 is slapping everyone in the face with two becoming one thematically in gameplay and story. The Ouroboros pairs, the fusion of 1 and 2's worlds, warring nations coming together, fusion of battle systems, etc. So yeah, she's definitely coming back. I would not be surprised if we see Rex in some form as well, depending on what happened with Pyra/Mythra.
I've been wondering if these "flame clocks" could have something to do with Pyra/Mythra since they seem so important.
Alvis will absolutely be back as well. Since he likely has something to do with the Conduits disappearance. And if the other two show up, Malos has to in some form as well.
Oh, and the big one I don't think I've ever seen anyone mention is Aion. Why do you think the world is called "Aion"-ios lol? It's not some coincidence. Offseer's are playing a part in the resurrection and Deus-ifying of Aion.
Noah and Mio's flutes each correspond to the color scheming of one half of Aion, then at one point in the story they swap flutes, signifying their "unity". Like, it can't get anymore obvious.
I thought about that too, but it probably won't be something that makes a difference in the end. Maybe a line of something because the name choice doesn't really matter.