Check out this post I made at RelicNews about an idea I'm throwing around. Basically, it would make it possible to create a set of missions located in a sector of space where players are allowed to choose the mission based on its X and Y position. I've shown in my other mods that it's possible to generate level and mission data dynamically, meaning it should be entirely possible to have the content of a mission change based on which mission - or which sequence sequence of missions - the player selects, as well as the location of the mission within the sector. Thus, you would no longer be limited to a linear, chronological sequence of missions for every campaign, but instead could have a sort of "strategic map" from which to make your selection.
This is really an old idea of mine, and the reason I didn't pursue it in the past was that there's no way to launch a mission from the frontend UI arbitrarily. You are limited to the Tutorial or Ascension (default) campaigns, and have to overwrite one or the other of them in order to get the "Start Mission" button-click in the main UI to register with the game. Basically, it's the same reason why all the custom campaigns out there need to be loaded from the command-line unless they instead overwrite one of the existing campaigns.
Why Relic decided to hard-code the UI in such a way when it's otherwise easy to reconfigure, I don't know. It's one of the several things they overlooked that I rather wish they hadn't.