It won't take any code changes, the secret isn't in the coding, it is in being just plain wierd enough, and have gotten lucky enough to get the inspiration while building a mission for someone else's campaign. One thing i learned in that campaign was what really set this idea into motion.
Each Episode will have a wrap up. You can be stripped of your command if you really blow it. Episodes 1, 2, and 3 are pretty much preludes to war. You gain command of larger battlegroups until you are pretty much in control of all your warships.
I just finished doing my work on aldo's Casualties of War, which by the way is a kick ass ride. That one will definately be coming out. I may even do some more on it, depending on what all is left, I want it done. And the campaign i wrote for FS1 is finished, though i won't publish it, all 60 missions complete with voice files. While i do understand what you are getting at, and agree, this will happen, even if i have to use the ships that we have in the game and just change the tables for modifications.
When we get done with this, i have yet another idea for something fun.