I'd like to also add that from my perspective diplomacy seems to be very stale in that there is not much to do outside of trading and even then its like pulling teeth to even get one deal passed unless you have high tech that is way above their means. Heck trading planets/ships/starbases do not seem to add much weight to trading. Three of my planets was not even worth one...starbase and I am in ok standing with this faction. Back to diplomacy why not have what is already there have a greater value like open borders, a faction/country would not normally have open borders unless there is something to be gained. Maybe have it where instead of both sides opening borders to each it is only one--so that it has more value and strategic use. The faction who opened there border can even get a slight increase in influence due to they opening of their borders due to the increase of vulnerability to their territories. However in order to make this work the AI would have to view the influence zones of factions as no go zones, or better yet both sides are allowed to--as long as they keep their borders closed to attack and destroy any entering ships aside from diplomacy/trade ships as if they were viewed as pirates. This way the borders are able to be kept protected, however destroying a ship would naturally cause the faction's ship to become displeased or angered and if given enough time of their ships or vice versa being destroyed this could lead to war. Some factions much sooner than others. The type of ships destroyed could also a greater weight than others, for example a lone military ship discovered and destroyed may not have as much weight compared to a destroyed colony ship due to the colony ship containing billions of citizens.
I think that adding this would make the game more interesting diplomatically since now you could protect your borders from being over run but at the same time you have to be careful since angering your neighbors may not be the smartest thing to do. Maybe also adding a weight that increases the AI's chances of not sending any ships to any zone if the the ships it sends into said zone keeps on getting blown up. At the same-time the AI should get mightily pissed should the player enter their own territories making it harder to trade and other such things.
And As Willywilber added in another thread. The AI, and the player ships should be able to defend themselves--I am not advocating for an automatic battle win. The two ships have to battle it out like normal, its just that the ships entering your zone/territory would be free game and vice versa if you as the player is entering another faction's zone.