12,000 years later, and humanity's technology has not advanced one bit. Neo-DEAVA still has the same technology as in the original series. Movie theaters still use film. They still can't clone a new eye for Zen Fudou or new arms for Donar.
So is Mikage a shadow angel? He seems to be one, complete with reality warping power and not having to open his mouth to talk, but nobody seems to realize this. While the shadow angels are mentioned it seems its been so long nobody can remember the fine details about them (or the events of Aquarion) only that they were a thing and humanity fought them. His people just seem to think he's some kind of shaman guy. No others angels seem to be around, and I don't believe it was mentioned just how he came to be beyond him being a reincarnation of Touma's jealousy. Which doesn't explain how he was apparantly born as a shadow angel after they'd apparantly all died out.
Aquarion ended with Aquarion and Apollo Sirius and Touma sealed into the Tree of Life to keep it going. So how did Apollo even die to be reincarnated, and if Sol Aquarion broke out then how is the Tree of Life not dead?
The Tree of Life did die, Aquarion was just holding the planet together. Presumably after 12,000 years the planet had long since stabilized and no longer needs Solar Aquarion. As for how Apollo, Sirius, and Touma died... they didn't have any food or water down there.