I like the way Descent: Freespace works, but I don't know how scientific it is, if at all. Basically, space travel is explained by the use of subspace, which is a higher-demensional, faster-than-light shortcut between two points in space. Pretty much a just-add-water wormhole.
The concept is not explained in detail in the game, but it is an important part of gameplay. Every ship is equipped with a subspace drive which enables it to do short-rnge jumps within the star system. Inter-system jumps can only be done through subspace nodes, which are large (compared to the fighters anyway- only about a mile or so across by my estimate) "holes" in space where two systems are connected by a subspace tunnel. Each system has from 1 to 4 subspace nodes, each leading to a different neighboring system.
This layout makes for very interesting tactics, because the nodes are the only feasible way of traveling between star systems. There are multiple courses to get to most systems, but not many. Therefore, subspace nodes are crucial military blockade points. The best way to defend a system is to secure all nodes in the system and heavily defend them.
Here is how it could work in-game: (this would only work on hand-made maps)
Coast becomes "planetary space", with very high movement points, say 6, to reflect complex orbital maneuvers required to move around in a system, and it would only appear in tiles directly adjacent to planets/asteroids/etc. All other "deep space" would be ocean, with a lower mp, say 4. Sea tiles would only appear in 1-tile-wide straight lines between two neighboring systems, and would have mp of 1. All ships would have very high mp, 12 or more, so that they could move a couple tiles in a system, and also jump through a node in usually only one turn. Deep space would be impassble to wheeled, and orbital-only ships would be wheeled, but could still jump. They could also possibly have lower mp and treat all terrain as roads, so they could move more quickly in orbit than big bulky capital ships.
EDIT: Make that ignore movement cost for coast, instead of all terrain as roads; I wouldn't want them to be able to jump and still have plenty of moves left over.
Any thoughts/suggestions/flames?
I'll see if I can catch a screenie from the game to show how the galaxy is laid out.