Well, if you have that many planets, yeah, I'd not want to deal with it either.
Decide now how many planets/system you want there to be.
I was thinking of MOO2, so there are like 50 systems in total or something. (and that's for multiple players to grab)
But if there will be a couple hundreds of planets/systems, then maybe as an Emperor, you just say "I want Military Production to grow by 30% in the next 25 years." And let the AI do it for you or something.