Had thoughts about this. One player is the first and last hero, the other player is the middle hero and runs the game. The runner also draws two cards at a time from the Scion deck, three at a time from the OblivAeon deck, and picks one that would be fun at that moment in the fight, treating the others as never having been revealed and sticking them back into the deck somewhere in the middle about. The player who has two heroes can also help a little with environment 2.
Actually I have a better idea. This way each player effectively alternates turns, with no doubling up. For example, the turn order might go:
Legacy, then Luminary
Guise, then Megalopolis
Progeny, then Freedom Tower
Dark Mind, then OblivAeon