Something just occured to me. Warning: This theory might not make much sense.
I've heard a bunch of theories that either a) Johnny K. Gambino WAS Meili or b) he was a descendant of Meili. How could he be a descendant of Meili, though, and still be human?
Answer: Meili hooked up with a human and that resulted in Johnny's birth, which results in Gino's birth, which is why Gaia shows him some preference.
Now, if Meili has hooked up with a human, who says Gaia hasn't done it herself? Or, pressing even further, who said that it was even a human? (That's probably a stretch, but it would explain some of Nyx's rather non-human looking features.)
And maybe Gaia was so ashamed of herself for doing all of this that she took it out on Nyx, thus treating him as an inferior being (the way she probably views most humans). She isolated her son to the moon because she didn't want Nyx to be anywhere near her, serving as a reminder of what she'd done.
Also. Perhaps, instead of Gaia having withheld powers and abilities from her son, the human part of him simply wasn't as capable of dealing with those abilities. That's why he had none.
TL;DR? Here's a brief, easier summary of the theory: Nyx is Gaia's child via a quick hook-up with a human (or perhaps some other mammal). Gaia was so ashamed of this that perhaps she exiled Nyx because she didn't want him around as a reminder.