Ah, I gotcha. To your questions:
The unclaimed planets would just be if you kicked the AI off and then didn't take it back (or if the IA kicks you off a planet, and you don't take it back yet). Basically, at the start of the game there are no unclaimed planets at all, they all belong to someone (mostly the AI), and then it's a matter of the destruction that happens over the course of the game.
But no, the AI never rebuilds command stations or anything of that sort -- if they did, it would be pretty impossible, given the current mechanics. There is some talk here on the forums recently about adding in a capability of that sort, but it would be more for experienced players. As it is, you're launching guerrilla warfare on the AI over an extended period of time, and you basically get to set the tempo aside from its waves, etc, against you. It's such a challenging game, in fact, that on difficulty 7 (where the "true" AI begins), most people lose half a dozen or more games before ever winning.
Granted, you can play on easier difficulties and have a much simpler time of it, but I get the feeling from your questions that you may be worried about the challenge level; if that's the case, you may be one of those players who quickly graduates to difficulty 8, even, but the game should be plenty challenging for you either way.
Let me know if you have any other questions (though I'm going to be off for the night, shortly), but hopefully that helps clear things up. The game is basically very asymmetrical. As one person described it, "the AI plays Risk while you play AI War." So while you're out trying to kill them and take over the galaxy using your mechanics, they use an entirely different set of mechanics to defend, enact various sorts of aggression on you, and ultimately try to snuff you out completely. And they can sure do it, too -- I designed and coded the game, and I'm on a grand losing streak of having lost the last 5 out of 6 games I've played with my three alpha testers. It's okay, we've had a blast on each one, but there's definitely plenty of challenge there.
Chris