All the discussion on Brad's last dev journal sparked another discussion about the right of passage treaty here at the office, and I have come up with another suggestion that I would like to put to you, our users.
Currently, you can attack a ship or planet, which causes a declaration of war. My suggestion is that we put a "Declare War" button on the foreign policy screen and make it so that the player must declare war before attacking any ships or planets. When you first declare war, any of your ships in enemy territory will be moved out of enemy territory, as it is when that United Planets issue is in effect. Since this behavior would now be standard, we would remove that UP issue.
This would have the benefits of not nerfing the engines while not allowing sneak attacks, and eliminate a lot of the complications that would come with trying to simulate borders in space. It's not a realistic solution, but it's one that I think will benefit the gameplay.
I realize that this might disapoint those of you who would like to see more meaningful diplomacy options, but I think that we can come up with other ideas for you.
edit: Sorry, it's doing that weird thing again where it shows up as black text on the forums, so I had to made the text blue so it would be more readable on GalCiv2.com, but I'm afraid if I make it white or something, it will be illegible on joeuser.