Rather then load multiple maps, a better way may be to take advantage of what's already in place. Save Files. Since all of the player information is recorded in these, if a campaign mode was to be set up, all that would really be required for a persistent style of game play would be to autosave when you quit the map (complete it), then recall the specific lines that state your credits, ore, crystal, researched techs, and ships and use those instead of using new values when the next map is loaded up. None of the information related to the planets themselves need to be carried over because you're in a new system.
In this manner, you keep your mobile fleet, you keep your saved income, and you keep your research. All that would be required is for you to take over a planet and start building your empire up again. Build new shipyards and research stations, get that economy going again and pick up where you left off. The only drawback I can tell so far is that P.O.S. percentage of income lost because of fleet research. I personally believe that percentage should be based off of the number of ships you actually have, not how many you could have. Granted, if you have no income you don't lose any, but if you failed to bank enough resources in the previous map, it could make the current one impossibly difficult to get enough replacement ships to the front lines early on.
