This is just me throwing an idea out, but how about this:
Perhaps one solution would be to add a way to access predefined maps and non-player controlled base screens directly on the Geoscape through the nodes that make up the ships, bases, waypoints, etc. Basically by adding a new node type for modders to be able to create and define new locations that can be added to the globe. Each one could then be linked to a custom base, map, etc.
To interact with the node you would do it through context-sensitive buttons in the pop-up dialogues. These would change depending on what the site has been set up for. If you click on the site on its own you would just get the standard pop-up with the name. But if you were to land a ship with crew at the site, the pop up will have the relevant buttons added to it.
If it's a friendly base for example, you could get a button to access the base screen where you could do things like buy/sell/transfer, refuel and refit the ship, etc. If it is a mission node such as a captured facility, you would have the option to launch a mission.
As with any idea this would be a lot of work to implement. Still it does seem it would be a fun way to add and access a variety of fan crafted content.
