I was thinking a solution might be needed too... though I did find it somewhat humorous (though it could get annoying quick).
I also figured it was player with a larger empire who had decided to create new little empires to engage in some sort of Guerrilla warfare.
On that note:
I find one issue which bothers me, is it is incredibly difficult to defend worlds. Especially with Imperial Guards, who appear to die off very quickly. I think they need a longer shelf-life. I've been moving thousands of Imperial Guards to my planets, but within days they quickly dropping to zero. Once an empire spans over 100 worlds, (actually even less), it becomes incredibly tedious trying to defend them.
And in the end, especially with the fact that losing a Sector Capital, means losing additional worlds, the only real strategy is to focus all defense on the Sector Capitals and setting all remaining worlds to build no defenses at all, as they really serve very little value in actually defending your worlds.
One other suggestion, is I think planetary defenses should be stronger and able to build more. Even by increasing the defaults, from say 5% to 10% of production, you still aren't able to build up defenses that will really stand up to any fleet. I think building a sprawling empire would be more rewarding, if in fact, your could actually defend it from attack. But as mentioned by others, the game currently really favors the offensive - especially an intense quick attack targeting all of an sector capitals (and capital) - while the other player is off-line
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