I tend to collect ships and usually use a small and fast ship to travel to where I stored the most appropriate ship for a mission. Right now I must come back to the place where I had to park this courier, leave for example the freighter there and go to another station where I bought and parked the battle cruiser.

How could I get all my ships into one station, preferably my own one as soon as base building is in?

Maybe hire Mercs without a ship remotely at that station where my empty ship waits to get a pilot. Or transport them as passengers there. Or use a remotely controlled autopilot which cannot mine, salvage or fight (we would still be able to automate transport missions with such a feature though).

In my opinion that's kind of strange in the X series, cause there pilots are mostly like cargo or for story purposes and the autopilot is too powerful (not the AI, but the concept). In Astrox people can be much more valuable than an autopilot, because of their skills and loyalty.