I just found out that the airbus is currently a unique, here's a suggestion: make the first airbus have slightly different stats, someone tweaked it, tuned it, whatever, compared to what you get through the car thieves, this way you can have information on your starting vehicle and you eventually can buy more as needed. Maybe allow the workshop to tune the new ones to the standard of your original, with the right research, so you don't need to fear selling it.
I also think that it would make sense to have the game progression largely based on your actions, specific research would move the story along and change how others respond, arm themselves, or just act in general. The basic idea is that the pirate crew are not heroes, they're not really reacting to a scheme of some villain, they are among the ones that the world is reacting to, very little at first, but eventually even the Star Gods may come to fear them... or just destroy them outright for being a nuisance. They are not an elite anti-terrorist/alien/heathen(cross out what does not apply) group, though they sometimes act in that capacity, how the world perceives them is up to them, or even if the world notices them at all.
Also, I seem to remember plans for different storylines based on what groups you align yourself with, be it the mutant alliance, the church, raiders, bandits, cultists of the dark gods, or even, heaven forbid, the traders. So having the set progression based entirely on time seems like it would cause problems.
Another option would be a middle ground with some things on a timer and others based on gated research.
Did this make any actual sense? I can't currently tell