A few ideas which may have already been proposed...I didn't read through everything...and keep in mind I'm not a programmer so I don't know which of these ideas are doable and which aren't. Thanks.
1. Friends and enemies alike should be able to enter water tiles within your cultural borders, regardless of open-border agreements, until a specific tech is researched BY YOU. My suggestion for this is Optics. So if you have Optics and your "friend" does not, you can enter their water squares without an open-border agreement and without declaring war, but they can't do the same to you. And vice versa if they have Optics and you don't. And if nobody has Optics, then all water tiles are fair game for travel. Battle conditions would still remain the same (you need to be at war to engage in combat, except for Privateers).
2. Open border agreements shouldn't automatically extend to air units. Nations should be required to sign an additional open air agreement. Stealth air units should ignore the requirement for an open air agreement. An open-air agreement should be signed with pre-flight civilizations, as well. Ignoring them shouldn't declare war automatically, but should come with an attitude adjustment...open air agreements should be required between nations once BOTH nations have discovered Flight.
3. As the manual for BtS states, if you have enough of an Espionage advantage over an opponent, then their spies cannot enter your territory. As far as I know, this feature doesn't work...it would be neat, though...
4. Civ should be able to read my mind and know when I am hungry, and then replicate a pizza and transport it directly to me...maybe make this part of the Star Trek mod?
5. New building - Naval base (or maybe give some of these functions to the Drydock, instead of a new building)
Pre-req. tech: ??
Functions: All tiles within that city's cultural border should get +x% bonus vs. naval units (I suggest +10% bonus). This should apply to attack and defense. And maybe (not sure how popular this might be), a naval base can take free pot-shots vs. adjacent enemy naval units (remember Coastal Fortresses?). And in addition, Naval base should have an x% chance of detecting submarines within its cultural borders (I suggest 10% chance). City can draft naval unit (this feature shouldn't be available until later in the game, maybe after Industrialization or even later, and even then only for a weaker oil-based naval unit).
6. New building - Air base
Pre-req tech: ??
Functions: Faster air-unit production and/or air units get additional XP. Increased combat bonus vs. air units within the city's cultural borders. City can draft air unit (a weaker Fighter unit maybe?)
7. New building - Army base (Or maybe give this as an additional function of a Military Academy, making the M.A. more useful for those who like Nationalism)
Pre-req. tech: ??
Function: Drafted ground units in this city get the same XP a unit built in the city would get, not half.