Realistically, I think that rather than changing Omnitron, they need to a) introduce playable answers to it, b) not make those answers in factions that are already top tier, and c) provide alternatives win conditions for other late game decks.
To me, this seems to be more an issue that most 'stall' decks have limited ways to win late game. Omnitron is basically the same thing, it's just that 'Genesis stall' has a strong win condition and other factions don't.
The secondary issue being the lack of ways to deal with it, but that seems to be a problem with the game in general - too much focus on characters/abilities, not enough focus on locations/artifacts. Then when there actually is artifacts worth playing, there's not much you can do about them.