Tossing some random thoughts out for people to pick through.
What if sensors/communications were a key part of the game? If your sensors are disrupted then you lose detailed information on what is going on in a region. Life on the planet would still continue, and they would carry on as they were, but if an enemy fleet with suitable jamming equipment got in range they could black out part of your map and allow a fleet to move without you knowing exact details.
Combine that with the long duration battles to actually conquer planets, and it gives a viable defensive measures with attack counters: Defender can strategically place their fleet that is moved to where they are attacked, while the attacker can strategically place decoy/jammer fleets to try and hide where the actual attack is going on. Of course, relying on building a fleet of jammers means you give up resources that could have gone towards your attacking fleet, which puts you at risk of being clobbered that much easier if you run into the opposing battle fleet.
Area control and surprises. What if fleets weren't always easy to see, especially for attackers? Set up sensor girds to better detect vessels entering your region of space, so the defender has the advantage of knowledge. Use some kind of webbing mechanic to allow a smaller fleet to delay a larger one, possibly giving the defender time to reposition and intercept, possibly having their webber fleet clobbered as the attacker focuses on the now exposed stop-gap. Attacking becomes more complex than simply assembling a large fleet and throwing it at the nearest enemy planet.