...ooookay, I'm not sure if this is even possible, or perhaps even implemented, since I haven't played all the way through XPiratez, but maybe this is something you consider worthy of pusuing.
I was thinking that since you are not the only pirate-y organisation out there (Raiders?), it might be interesting to have other pirate bases that you can raid in order to obtain slaves or runts or perhaps even brainers?
----> this leads me to another point:
I think that the brainers are far too "cheap" in the game. I mean, your research facility can hold only a few, and they are extremely important, so why can they be bought at all? within the setting of the game, brainy mutants suitable for true research should be a valuable resource, and a group of pirates should be happy to have maybe two or three of them... finding more should be more difficult than just going to a market, shouldn't it?
perhaps finding more of them should work more like paying a market fee to obtain information about where you might find one, spawning a special mission that allows you to go and try to steal one from another group of pirates... if that's at all possible within the extended code. of course, that would make the game even more RPG-y, but that's a good thing, isn't it?