Yozora tells Sora he doesn't actually look the way he appears to Sora in truth, and that Sora is "recognizing" him as Yozora. This means this boy is probably someone else entirely. This is further backed up by the the Nameless Star claiming to be waiting for him and that his heart is being covered by another.
I think Yozora is actually none other than Brain.
I still feel that the Nameless Star is Subject X, and I still think Subject X is Skuld. We don't know how UX will end, but at the very least we know Brain and Skuld do know each other, and it is possible that after whatever occurs to scatter the Five across time, Brain would try and hunt her down.
Now why would/how would Brain become Yozora? Well we know that in the world Toy Box, Yozora is from a video game, Verum Rex.
And it just so happens that over in UX, the player is currently exploring Game Central Station... a world that connects several other worlds based off video games...
What if Verum Rex is part of the GCS and we just haven't discovered it yet??
So far the story elements have hinted that the connection of the GCS to Daybreak Town is critical to how the five escape their data prison. Right now this theory is more of an idea than a concrete case.
Anyone have any guesses as to who he might really be?