All right, first of all I should say I don't think I could make this change myself---I am a writer, not a programmer---but I know it is possible, because I have seen (proprietary, for-pay) RTS games that do this.
This would be the ideal campaign system: Not a simple linear "mission 1, mission 2, mission 3", but a fully-featured campaign editor that allows the successive mission to be chosen by triggers during gameplay.
Starcraft did it; Warcraft III did it; even that obscure Brazilian game Outlive did it. It can be done.
Even better would be some capability of carrying units from one scenario to the next; but if we can't do that, it's not as important.
Why do I need this? Because I, along with some friends of mine, am trying to design a game. I want to mod an open-source engine, and I need one that's extremely flexible---you'll see why in a moment. Glest has everything I need, except this. If Glest is to be the engine we use, we need the capability to choose scenarios based on in-game events---it's a dealbreaker.
So let me sell you on the idea: The working title is Butterfly, after Lorenz's "butterfly effect." I'm picturing an intro sequence where a little butterfly alights on a leaf, and then gets crushed under the foot of an assault mech.
The game is all about timelines. You start out circa 2040, at the start of a massive nuclear war. The world's population is devastated, and you decide that it is time to use a technology you promised you never would: time travel. You attempt to travel back to 1945 in order to prevent the Cold War, but the time machine malfunctions and sends you further back, to 1813 in the middle of the War of 1812. You decide that since you can't really control the machine, your best bet is to change history completely, prevent the United States from ever becoming a superpower---and that means helping the British win. This, naturally, disrupts the entire course of history, which you are now tasked to repair---or even improve.
Whether and how you complete missions alters the timeline, sometimes subtly, sometimes dramatically. The game plays through five distinct technological eras, with the fifth era being a futuristic era roughly 2040-2100 (hence the mechs). You have the opportunity to move units from one era to another---but the more you do this, the more the timeline grows disrupted, until you have anachronistic universes in which the world is ruled by Iran and cavalry are carrying laser guns.
There is also an optimum future, one in which you manage not only to repair the timeline, but in fact to improve it; you prevent WWII, the Holocaust, the Cold War; you bring about international peace and prosperity; you start the process of interplanetary colonization. That's the only way to really win the game, though there are several other "endings"---with time travel, there is no such thing as an ending!---that you can bring about, including one where things are back to normal except sans nuclear war, and one where you just utterly fail and everyone dies.
Now, does that sound like fun, or what? Glest clearly has the functionality we need to create the units and tech trees; in fact, Blender integration is vastly superior to anything else we've seen, and makes Spring's use of Total Annihilation units look downright childish.
But we need campaign-editor functionality, or our whole project is dead; the whole game depends upon a nonlinear single-player campaign. If I knew how, I'd program it myself; but I don't, so I'm hoping that by giving all of you a nudge you'll find someone who can.
