It's been happening to me too. Pretty damn irritating, and its so easy to counter it too.
Bugg Superstar
The fleet cap is and should be tied to the economy and research and not to how many planets you own. It makes it much more realistic. For example, in a small 2vs2 game I played the other day, I ended up with only four planets, while the enemy owned 6 or 7 planets each. My ally owned something like that too. Still, I was the number one economy(and technology) powerhouse, something that allowed me to have a bigger fleet cap than my enemies while still having a strong income of resources. I managed
I think the superweapons are there just to soften up the enemy. Even though the AI recolonizes the planet, it will take a long time to rebuild it to its former glory. This hurts the enemy's economy, giving you an advantage when invading him. btw, this is my first post, though I've been around since beta 4. So hi everybody!