One thing I'd quite like to see implemented is a basic blockade system.
Because really, if you've lose all control of your space to an enemy, then your internal trade and communications will be devastated. Presently, not so much. I have AIs declare war on me long before they have transports, I have them successfully occupying chunks of territory... and I don't need to worry, because they can't actually hurt my planets in any way yet. I understand that organizing 3 billion soldiers or whatever requires a tech gate, and I'm cool with that, but really there needs to be some genuine threat to the enemy's production from losing control of space.
Nothing major - just a system whereby, if the enemy manages to put a warship into unopposed orbit of your planet, you get some negative pop growth or reduced production. Or both. If an enemy warship is adjacent to an undefended planet, then that planet ought to be slowed down at least a little by its presence.