I thought it was mentioned (nad makes some sense to me) that starships just don't realistically take any damage from the PCs 'light' weapons. They just simply bounce off or do superficial damage.
I suppose if you consider different parts to be similar to a bulkhead you mentioned, then it is effectively immune to PC fire in a realistic way.
The amphibious trait mentions it doesn't take the -2 penalty underwater for bludgeoning and slashing damage. It doesn't mention ranged attacks, but I would presume that it would negate the cannot attack and the people that made them thought the trait did negate it.
Unless someone else finds something more specific.
A balancing act could simply be class feats that give you a bonus with a penalty linked to it. Or some system of picking drawbacks in return to extra stuff, but not requiring it or needing to track it every turn.
Say you take a drawback of -10' speed for some DR. Or maybe full BAB but in return you take extra damage etc. Then have a limit of how many drawback/benefit pairs you can have based on your level, allowing you to decide how much to power up at the cost of certain things happening.
When I heard about this, I imagined something that was able to gain some form of monsters abilities, even if only for a short time (void adaptation, starflight, trample, etc).
After reading it just seemed like a complicated mess that didn't really have a strong idea of what it was about. I agree with some of the points above on this. I just wanted to be able to grow wings, extra arms and so on.
Not to derail things I won't include a link, but if you look for Liber Genus by me in the 3rd party section here there will be a link to it. Just the ghoul for now, the vampire is the next one I will be releasing once I take a second pass at the feats and set it all up properly.
Maybe use the VP system initially to allow them to build up the defences using whatever rolls you feel are appropriate. Then have a decreasing VP using that initial value as you mention to show the undead beating them down. Allow the PCs to earn more VPs by shoring up defences etc or making combat rolls to indicate them fending off the enemy. Those that use spells in interesting ways could add more points to the total as well.
Maybe have 1 combat encounter for a boss that could modify the VP total depending on how quick they deal with it.
As for skills they could use pretty much anything that makes sense. For example religion could be used to set up anti-undead wards, society for placement of barricades etc, arcana for setting up magical strengthening of walls/doors, athletics for moving barricades etc around, bluff could be used to set up distractions like fake soldier dummies and so on.
Yeah I thought part of the reason AoN became official was so they got material early so it was ready to go live on the street date. Kinda annoying, even with owning the books.
As for what I would like, maybe more symbiote-like creatures (there was one in a past AA, but cannot remember its name) would be interesting.