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.
It could be that the near-destruction of the world resulting from the death of the Tree of Life knocked humanity back quite a ways in terms of technology. Frankly speaking, the Earth was wrecked at the end of the first series.
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.
Mikage mentions near the end, when possessing Zessica, that it's been a long time since he had a "real body", suggesting that he's just a spirit. The shadow angels in Genesis did possess physical bodies, so this suggests that Mikage is really more like a disembodied piece of Toma's soul.
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.
It's also possible that the strain on them from pulling the Earth back together was too much.
So what was Zessica's actual promise to Mikage? Either I missed it or it's not in there, because I don't remember her ever promising him anything.
He opened the gate for her so they could go to Altair to find MIX. Mikage being being Mikage, none of it was remotely fair. He just appears as she's moping, says he'll make a deal with her to open the gate to Altair and then does it and says they have a deal before she even really knows what's going on. Not to mention they don't actually retrive MIX during that time. In fact based on how easily she forces him out of her once she gets her head back in the game it's possible there was no deal in the first place and he was just screwing with her, and could have possesed her at any time as once she stopped moping he no longer had any power over her.