Good idea.  

It might be viable in a future expansion pack, actually (or even GalCiv III). There isn't much chance it will get into Dark Avatar or the 1.3 patch, though.

I see two basic ways to go about implementing it. The first way would just be 'fluff': ships randomly travel back and forth between planets in your empire provided they do not cross over into enemy territory. These ships would have little to no impact on the gameplay (maybe they could be targeted to declare war or something, and some may have VERY light weapons, but that would be it).

The second way would be much more in-depth: a new ship module (Domestic Trade or Travel Agency, perhaps) would first have to be created (and you would need at least a little technology, probably in Logistics, because this focuses on your empire's actions and not your interactions with other nations). This ship module, when equipped, would allow the ships using it to establish Civilian Travel Routes. Once a route was created, the ship would disappear and a steady stream of civilian ships (their number, frequency, and effect dictated by the average of the planets' quality and population) would travel back and forth between the two planets (or more, if possible), much like foriegn traders. These ships (for the most part - some might have very minimal armanents) would be very vulnearable and might travel at slower speeds than even Freighters (because they are civilian ships who don't generally have access to military technology). However, each planet would recieve a bonus, probably in the form of increased population growth and an economic percentage bonus. As your empire gets increasingly advanced (better engine, hull, logistical, offensive, defensive, life support, and trade technology may be factors in the equation) the 'Private Sector' begins to pick up on some of the technology, with the result being improved civilian travelers. It would only take a few civilian causulties, or even just enemy ships remaining near the travel routes for a few turns, to scare the population and close the route.

That idea probably won't be implemented, but it doesn't hurt to post ideas, right?

The initial idea was that it would look somewhat like a trade route but its establishable between any two installations (be they alien planets, or starbases). I think the main benefits of this would be

A) It would have increases in several domestic ways. It would be a bonus to the economy to have people flowing. Also with accessible travel it would increase moral. And if you establish these 'space highways' with aliens it would improve relations. Think of Canada and USA, and alot of europe. With open borders there are good relations.

It would provide realistic defense, because when your defending yournation you dont just protect the hubs of commerce and enterprise but the entire area. Because if your civillians start getting blown up moral goes down (and if your using any goverment other then imperial) people question the war, and future wars.
Also it'd be nice to have battles devolp in places other then planets and leading to planets. It makes the war more widespread through your nation.