*yogi*

In my experience, I have also run into this problem of advancing from startup quadrant where you start with excellent reputation into areas of the 3rd and 4th quadrant towards core and realizing I need captains and running into Reputation issue. Now, I always remember to purchase a couple before leaving the friendly Rep area where I start. That will solve that issue. But you will need to plan ahead and decide where you will be going and need to raise your rep with a new faction. I think the Reputation aspect of the game is a very important core feature - you could not have a functional universe without it - to decide who is at war and who is friendly and gets access to the best turrets etc.. And if you do not already know, the "Free Slaves" mission randomly given by stations in their bulletin will allow you to basically purchase 15000 rep for around 200,000+ credits by paying off the pirates for the slaves. Doing that a couple times gives a big boost to Rep. Selling ores/ items to a faction also gives a big boost. Hope that helps.