Well, you see, the command stations provide tachyon-based FTL communications across local planetary systems, which is in turn linked into a galaxy wide comm-station communication grid. Which explains why ships go slower on planets without a friendly command station. It's communication lag. Anyone buying this? No? Well, it was worth a try.
I like to amuse myself with trying to come up with technobabble explanations for gameplay conventions, but even I can't figure out how to reasonably explain a speed limit. Closest I can think of is starting with the assumption that every ship travels at greater than c, and the amount that they are able to exceed that limit based on their own sci-fi magic engines is what we see reflected as their max speed. But then I hit on the fact that every battleground is only as wide as a few planets, tops, so any ship traveling even at 1/2 c would zip past in seconds. And then I give up and go shoot the AI some more.