Let me start this off by saying I know it would require an almost prohibitive amount of work. But, I think it would be amazing to see an AP focused on the guerrilla war between Nirmathas and Molthune where the PCs could end up fighting for either side. It could be a situation where the PCs start off knowing they'll fight for one side or they might be forced to make a decision partway through the AP.
This would be tough to do, since you would have to generate material that might apply only for PCs on one side or the other. But, there could also be material that would overlap. Maybe there is an artifact in a dungeon that would be useful to both countries' war efforts. Or, there could be a situation where one side is trying to take a fort while the others are defending it.
There's not a lot of material on the Nirmathis/Molthune war thus far (I'm only partway through The Wizard's Mask) and it would be awesome to be able to create material where the PCs could influence the course of the war to go two different ways.