Theoretically, in the late game, all factions are roughly equally strong, except for the Fortress and Necropolis. The Fortress, perhaps, is the strongest late-game faction; its runes are simply too overpowered in the late game (specifically, the resurrection rune with the "fight to the last" mechanic: you attack the Fortress units, attack, and only one nearly defeated unit with 1 HP remains, and then, bam, almost half of them are resurrected at once).