* Put the engine upgrades into piloting instead, and make autopilot its own subsystem. This is really just a flavor change, since there's no functional difference outside of the first bullet point. Autopilot should allow you to jump without someone sitting at the helm, perhaps with an additional delay.
* Alternatively, if the preceding changes are too radical, give ships a "power core" room which can be damaged to reduce the overall power available.
* There should be better insight into the sectors you haven't visited if you have scanners/maps. "Potential ship detected" means (in my experience) that you will be attacked immediately, and often, there's a ship when no potential ship is detected. Long-range scanners are useful for detecting hazard regions and that's it. I might add information like "Mantis ship detected."
* More systems should be mannable. The artillery system is an obvious one. Droid control would be nice, too (increases droid speed?). As it stands, you basically have four crew members permanently stationed and the rest just sit around waiting for invaders (except if you get a spare Zoltar, who is happy to sit in your O2 room or something).
And if I could make those changes, I would have zero complaints about FTL.
