The tower defense elements basically boil down to the periodic waves that the AI launches against you. You can affect which planets they can launch waves against by destroying their warp gates -- lots of strategies surrounding that, and plenty of apt jokes about the enemy gate being down. ;)

In terms of it being literal tower defense where you have things that can't move, that's not at all the case -- there are fixed-position turrets in this game like in most RTS games, but you don't have to use them. THAT said, turrets are a good investment because for the cost of building them they provide more firepower than your mobile stuff (with the downside of being immobile), and they have a really huge range so it's not like in a real tower defense game where you have to line them up along paths, etc. It's better to set up "rings of death" around wormholes, or to use forcefields plus turrets around your key things you're trying to defend, etc. You can use minefields, tractor beams, gravity beams, and so on as well to accomplish similar things -- many strategic options there.

One of the big long-term things you have to manage in this game is how you allocate your resources. You're trying to attack and defend at the same time in many cases, and you want most of your defense to be as automated as possible for small AI incursions. That usually means a combination of mines, turrets, and mobile ships -- and definitely tractor beams -- on your border planets. Then your mobile fleet can mostly be used for offense, only returning to help defend when something really dire happens.

But people play all sorts of different ways: some use massive starships to do raiding on the AI while keeping the bulk of their fleet at home to play "catch" with the AI ships that get stirred up by this. Others do half-raids against the AI and then fall back to the safety of their own turrets to try to trap the AI (though the AI is often wise to this, resulting in some interesting back and forth or the AI going around in an unexpected way).

Reviewer Tom Chick called the game a "grand strategic tower defense 4X RTS" (http://www.crispygamer.com/columns/2009-08-13/rush-boom-turtle-and-now-for-something-completely-different.aspx). As he basically notes, the game is all of those things but none of them. It isn't a tower defense game any more than it is a 4X game or a grand strategy game. And it's not really a true RTS either, although it controls like one. It's something that exists in the space between all four of those subgenres, and that's what makes it a little hard to describe.