This does sound interesting. However, there are lessons to be learned from other games which had this (supreme commander for example). But let's adress the obvious question first:
- How do you end up in a hard to defend position, or bad spot with your immobile command station, when you can freely place it at the games start?
There is a lot of strategical choice in your initial home planet selection and having a mobile command station will dilute this. Just want you to think about it. That is all.
... and now to the lessons:
1. A combat-ready king is often nothing but wasted potential.
In games like Supcom where you have a mobile ACU which if dead ends the game for you and which has some very decent fighting power is often left even behind the last line of defense because the risk of losing it is simply too high. Unless you make it as durable as a golem there is no way people (generally) are going to risk losing it just to get some extra dps. Slow and steady wins the race. Why take the risk? Not even the fact that your ACU has an ability with unmatched power (overcharge) could lure people to use it offensively unless as a last ditch effort or during the very early stages of the game where there are no armies that can contest the king.
So what the guys at Gas Powered Games did in their sequel was to
greatly increase it's mobility. Through extensive research (and costs) you could unlock additional movement abilities which almost garuantee you being able to disengange if something goes wrong or you lose control of the situation.
I think this is something a mobile, combat oriented home command station would require too - especially in a game like AI wars where one of the AI's core traits is being unpredicable. If you move your HQ and the AI all of a sudden throws all the threat and strategic reserve it has at it you need to be able to escape (unless there is nowhere to escape to). Otherwise you shouldn't have moved it in the first place which defeats the purpose of a mobile HQ.
2. Some people still didn't like the idea- so they added OPTIONS to trade combat power for economical boost.
I think this is something AI War II could use as well. Something along the lines of "permanently settle your HQ - get an economical boost (like an extra generator) in return".
Then again, if you're fine with another ship which is "useless" 99% of the time but provides you a spectecular last stand during the other 1% then perhaps this is just what the game needs. I can't say which one I prefer. It's just important to me that you consider both aspects.
My 2 cents.