I guess I'm just stupid, but why is having to dock and bribe an official such a terrible thing? IRL, it costs money and time to get through Customs... you have to have a passport, which ain't free, and you have to deal with Customs officials who check your vehicles out at the borders, at least here in the U.S.
To me, it's little touches like that that actually add a lot of reality to a game- sure, it's annoying, but if the game designer is smart and savvy, he/she won't design the game so that you're crossing borders every ten minutes.
The real problem with this idea is that if you did it with the FL universe set up in the silly way that it was done originally (which seemed, at least to me, to be designed primarily to waste players' time as much as possible), then it'd get old fast- most of the halfway-decent trade routes take you through multiple "nations" with neutral/semi-hostile areas between them.
In a smart and sexy SP mod, there would be plenty of reasonably-profitable routes within every nation's borders. You'd cross national bounderies only for the following compelling gameplay reasons:
1. Because you wanted to see what was over there. This is assuming that in your smart and sexy mod, there's a lot more to see and do than there was in the original game, which was, to be honest, pretty empty and lifeless, aside from random encounters and the occasionally spectacular scenery.
2. Because you could make the HUGE fortunes required to buy... whatever was important to buy, by risking a very dangerous trip through the neutral areas delivering whatever special technology/delicacy(don't knock food, Europe conquered much of the world in search of spices)/illegal substance that could make you rich "over there". There'd be the extra-special tensions generated by police scans... if you made that Faction's police too angry, then the price of the "customs bribe" would get huge
3. Because you're a wanted felon in the nation you just left
Basically, I think this idea could be great, in a mod that finally "got it" about what was wrong with FL SP, imho: it isn't about more "uber ships" and more "uber guns"... it's about having a universe that doesn't seem to be utterly lifeless and dead.
For example, y'all know that you can use custom soundtracks for a given Zone, right? So how come I have yet to see a mod that has, for example, a Station or Planet with its own special soundtrack? For example... it'd be awesome to see a Space Diner floating above New York, with 50's rock n' roll and a bit of crowd noise mixed in playing as you approached the rows of parked (ok, either moored or placed) ships and landed.
Darnit all, this makes me want to start working on my mod again, hehe... my mod helps me to gradually erase FL's empty and boring universe, even though it's probably still pretty opaque to everybody else thus far