To be quite honest, I am glad the "no sneak attack" proposal is dead. While the AI has trouble using it, it is still a valid tactic. Sudden, unexpected attacks are simply a fact of military strategy. While two massive fleets lining up on opposite sides and charging each other is certainly an option, it isn't the only one.
What this idea would do, I think is limit the options of players who don't build massive fleets. Asymmetric warfare is one of the things I like about Gal Civ 2; I can take a smaller and more mobile fleet into a race I want to go after, hit weak points without warning, and keep my fleet out of range of their heavy guns. Why would I declare this to my enemy, run outside their space, and run back in again for this style of warfare? It could still be done, naturally, but less effectively initially making other styles of warfare than "whoever builds the biggest fleet wins" less practical.
One thing, I think that is important to remember is right of passage treaties are wanted for more reasons than just one. Many people were asking for them not to prevent sneak attacks but for other uses. Personally, I want them because I find it ridiculously annoying that the enemy can move ships through my space at will, colonize planets in the heart of my territory because I missed a Class 1 in my gigantic map because they don't show up at the most zoomed out levels, or conduct a war with another race halfway across the galaxy through my backyard.
I'd like to see an option for open or closed borders and also right of passage treaties so that you may open them for races of your choosing. Closing your borders has the effect of cutting off trade except with those you have the treaties with, but, on the flip side, any ship of theirs in your space can be blown up without declaring war, thought it will cool relations with whoever's ship you just blew up. Naturally, closing your borders to them will make them close their borders to you. Hopefully the AI can learn from this and will attempt to avoid your space after losing some ships there or better arm the next group of ships. One of the things about this I like is you still can only control as much space as you can police. If you don't have enough ships to shoot down interlopers, or your ships are too weak, then the closed borders policy will hurt you rather than help.
You know those races in Star Trek, the cagey ones who close their borders, admit nobody into their territory, fiercely defending their space from any and all who try to enter it? I want to play that race and at present, it just isn't possible. In order to do it, you effectively have to declare war on everyone which tends to end badly. Further, this could be a mechanism to further differentiate the races in the game. The ever diplomatic Humans might maintain an open border policy with everyone to facilitate talks and trade. The less friendly Drengin might close their border to all except those they are allied with in a given moment. Consider, if you send an unescorted colony ship into a race of evil reptiles determined to enslave the entire universe, are they A.) going to let it continue on it's merry way to colonizing a world they can strip mine for resources or B.) going to scrap the ship for parts and dump the occupants into slave pits to build more ships? I think this option could be used to reflect that.
One note I will make though, is that those races who do choose the closed border policy should have some effective method of continuing on without trade. Perhaps salvage ships, which, when accompanied with fleets, get back some percentage of the value of the ship the fleet destroyed in credits. This could make for an interesting challenge to the player - do I close my borders and recycle the ships entering my space for that money or open them for the trade income?
Another implication of this is further expanded diplomacy - demands you close your borders to another race's enemy or to open your borders to their freighters lest they declare war and open them for you. UP resolutions could exist regarding open border policies, such as a resolution for the benefit of galactic commerce that all races open their borders. What does one do about planets in other territories? Unless you expand your influence to encompass them your enemy could take your entire planet without declaring war.
Other options for limiting the power of closed borders (if loss of trade and difficulty exploring other race's space aren't enough) could be things like lowering influence due to decreased contact, lowered diplomacy due to perceived distantness and coldness, lowered tourism income, inability to use special treaties like research due to the inability of other race's scientists to enter your space (except for those you have right of passage treaties with), or other things others may think of to add disadvantages to isolating yourself from the rest of the universe.
Anyhow, these are my rambling thoughts on the topic, but I would very much like to see some mechanism by which one can play an isolationist empire even if these ideas are rejected for whatever reason.
Edit: In retrospect, this actually would do something to limit sneak attacks as those you are attempting to attack can pick off anything you send into their space if you don't have a right of passage treaty with them. It won't end it like the original proposal would, but it would still give the AI a new recourse to fight back. You know that warning it gives you about it knowing what you are doing when you send too many ships into their space? What if they responded by closing their border to you and blowing up your ships? Or if you don't have open borders with them, just pick off your ships as you send them in.