I think the Imperium will win out. If the Primarchs return or the Emperor awakens, a re-energized, stronger Imperium is posible. Plus, if (and I said if) the Emperor could reunify both the loyalist and traitor Space Marines, there would be no stopping humanity.
Barring that, Nids and Orks are the best bet to win out. Their numbers are too great for the Imperium to deal with, unless all the Space Marines were united against them.