I have played on other exile servers that featured a Virtual Garage via the XM8 tablet where you can store and retrieve vehicles from the flag at your base. If this feature was implemented, it might save on server performance as the server would stop rendering nearly as many vehicles that are just strewn about the map. I don't know (practically) how this would affect server performance, but just an idea.
You can impose limits based on what level the base is. Like Base Level 1 can store 2 vehicles, Base Level 3 can store 5, etc.