I had this thought in response to a comment I read on the forum in relation to how ships always spawn at the bottom center of the map.
Basically, the concept is a new type of beacon would be added to maps, called a hyperspace beacon (or something like that). At the start of a game, you would automatically own one of these. Then when you start the game, your ships warp in to wherever the beacon is. Also, it would be possible to place more than 2 (2 would be the minimum: 1 for you, 1 for enemy) and any other waypoints would be neutral. during the course of the game, you could capture these and when you went to call in reinforcements, you could select which beacon in your possession you wanted the reinforcements to warp in to. (at the start of the game, there would only be one available, unless the map designer decided to give you more).
This could also be used for the campaign layer, as the defined point where you warp into a system.