Giving way to an insanely diverse universe? That's the plan. :D I'll be doing everything I can to make things as variable, unpredictable and diverse as possible. And NOT like Spore, where everything may look different but it all acts exactly the same. (Also true of Starbound, though it isn't nearly as much of a problem there.)
If the cat and I can work some serious magic, I dream of the possibility of landing on a planet with great canopies like nothing you've ever seen before, and as you walk beneath them you see some random Fauna hanging from a vine by its teeth/teeth-like-apparatus-or-feature. (Which when it sees you, looks shocked, falls off the vine and runs off to hide in whatever way the species has evolved to protect itself.) In other words, vast ranges of behavior and characteristics for both Flora and Fauna, creating a universe where there is always something new to find, and they're interesting enough to be worth finding. All that being said, that's just a dream, my imagination let loose. For now, better to focus on the more immediate matters. Right now, the focus is Fauna.
I would love to have enough depth to the NPCs that you could set up a station that basically runs itself, and runs like clockwork. Even better, one that can react to different situations, such as telling crew or ships to only be sent out if they are in good enough condition. (As you mentioned.)
Things like this can actually be surprisingly simple as long as the foundations are in place, such as the ability of the NPCs to take the commands and do things like pilot ships, or dock them. Mix it with some basic priority systems (so NPCs act based on which action that needs to be done is highest priority on their list), the ability to coordinate (have stations/groups send certain set numbers or percentages of available NPCs to do tasks, to avoid having some problem come up and suddenly every NPC you have runs to fix it), and the ability to have it manage NPCs based on location, condition or settings (so if something needs to be done by a few engineers, it would find the closest NPCs who are both engineers - as opposed to soldiers or something - and in proper condition to do the task - such as not in critical medical condition or busy with a much higher priority task) would allow amazingly effective and detailed NPC activity. (This is not a statement of what will be in the game, rather a discussion on NPC artificial intelligence programming in games as it could theoretically relate to StarMade.) I can't say exactly what you should expect from StarMade's NPC control and AI, but I'd certainly love it if what I just described came to fruition.