The problem with time limit games is that victory and defeat can often seem arbitrary. You'd need a better system than just "who controls the most planets at time X" but I think you already realize that.
The whole problem stems from the fact that no player has a decisive advantage (otherwise we would expect a "gentleman's surrender" so to speak), so the game drags on. But if no player has earned a decisive advantage, then it's entirely arbitrary to award the victory to either player. While one of them may have an upper hand, they are certainly not "winning" yet.
What you are suggesting would be similar to "take, and hold". Cap certain number of key worlds, and hold them for x amount of time. If number is capped a victory countdown would begin.
Wouldn't work; early game starbases (particularly Vasari) are balanced on the presumption that you can ignore them and attack a different planet. This would revolve around whoever starbased the target planet first.
Also you can have a fixed time limit. and victor would be determined by a combination of factors. Like worlds capped. Enemy ships killed vs How many of your ships that survived. How much research. Etc. etc.
That's still an arbitrary "score", doesn't solve the problem.
Can also do cap ship assasination. a finite amount of pre built caps, and your goal is to kill as many or all enemy caps while protecting your own.
But often times you can go for hours without even killing caps. Many players are good at keeping them alive, you know.