Alright - so after the Avernite/Empire War and the various atrocities committed by the Empire I say screw making Peace with Empress Prazac, helping the Empire, and settling peacefully. The monster plagues put Avernum in a perfect situation to get some REAL vengeance - so for starters the new Avernum III should have the option to wage war against the Empire as an alternate story path - various things I would donate half my liver to see put into the game:
1. Ability to engage and eventually defeat the Empire Third Army through a long battle of attrition.
2. Alien Beasts escape Quarantine - eventually ravaging Blackcrag and evoking a military response after two years into the campaign.
3. Monster Plagues Evolve to become more Vicious: ie Alien Slimes roving around - Troglo/Giant War Bands that invade and occupy whole towns
4. Ability to Raze Towns: If a towns population is wiped out by force the eradication of the town can be completed with Move Mountains or occupied by Avernite forces/civilians
5. Dark Wyrms Hunt: Eventually the Dark Wyrms and Drakes/Dragons will emerge to hunt for food and treasure - which they might find on your collective corpses if you're not ready
6. Negative reputation: Killing Empire Soldiers and Civilians earns negative reputation that will eventually illicit attacks from the Empire.
7. Initially your party and Avernite forces are attacked on sight - situation can escalate to Empire Invasion of Fort Emergence