I prefer to see a territory system implemented ALA Civilization series, where your colonies expand your Empire's borders, where the only ships allowed in those borders are your own, and unarmed civilian ships of other Empires with whom you have a trade agreement with.
I would personally object to this, as far as reality is concerned, there is nothing physically preventing you from entering their system with warships.. .Such a limitation would be purely artificial...
A compromise, perhaps, would be rules of engagement.. .For example, a neutral fleet enters your system... you could have standing orders for all military ship to engage them, as they have no business being there... Seems like a bad idea though... as not only would you lose most of your ships (unless you have a fleet there) you will also invite war...
You forget that in the Civ series it is in fact not artificial, you can force your units into their territory but it then makes you declare war. Which has obvious consequences. This mirrors real life. Countries have borders, but every inch is not being guarded. However once military forces are detected moving across, war is automatically assumed.