My idea is that every empire has one that must be protected. Losing a capital means that you cannot collect resources and you lose contact with other races until a capital is restored. Also, it increases the odds that your empire may fragment into seperate nations. This may be something that could be modded.
I think Aaron has said that this will not be a feature in se4 possibly se5 but the AI doesn't handle it very well and it makes it a lot easier to cripple an enemy so it will definitely not be in se4
Homeworlds in Proportions is close to what you want. Lose you Homeworld and game is pretty much over unless you retake it ASAP or conquire somobody's else
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It is forbidden to kill; therefore all murderers are punished unless they kill in large numbers and to the sound of trumpets. - Voltaire