[johnny]

I think some gods would have remained on earth (these would be the "unlucky" ones, as if I recall correctly Egyptian mythology believed the afterlife to be a "true" life and earth was something of a purgatory. I could be remembering it wrongly, though, so if any Egyptian mythology knowers are out there, do correct me) but the stronger of them would have gone into the afterlife. This allows us to have the vessel gods as well as the demi-gods who know humanity well, and the more elitist "afterlife" gods who are jealous of humanity as well as unfamiliar with it.

For the sake of the plot, we can't have the antagonist gods be earth-bound, or else they would be accustomed to earth technology and that spoils the whole "they attacked because they were jealous and fearful of humanity moving on without them" plot thread.

Probably, the strongest of the gods would have gone into the afterlife, and that might mean the most "well known" of them could be our antagonists. It would probably take gods like Ra, Osiris, Set, Iris, etc. out of the role of "protagonist" (and therefore truly playable character). We might figure out a way to save one or two of them to be vessels, though, if someone really wants to play them. Keep in mind during characterization, however, that Egyptian gods are portrayed as extremely well-balanced and neutral, so even a god like chaos-driven and murderous Set could be a good, protagonist vessel if done right.