The bottom line is that Illuminate game-play would need to be improved for wars to be shorter. Cyborgs and Bugs have no problem reaching completion. However, since there is a substantial player-base which plays Illuminate, it would be unfair to overhaul Illuminate game-play for the benefit of those who regularly play Cyborgs and Bugs.
A simpler change without changing or adding any new game-play features fundamentally (aside from nullifying/ removing faction locking) would be to make home-worlds last indefinitely if they are completed (completion of a home-world would generate a new home-world with a different environment). If a home-world is lost, the game functions as normal, reverting back to a ‘region’. The war ends when home-worlds in every faction are reached, or when Super Earth is destroyed as normal.