They more or less use the MED, I think. Most of the extra cinematics and effects (like camera panning) are done through external files (the ones for the campaign maps are all packed into a file in your game folder). The campaign is set up through some kind of text file (I haven't tried using it though).
The rest I'm guessing is hard coded into the game, but most of what Nova did with each campaign can be done by mapmakers too. A few things we don't know how to create, like AI Node files (AIN). AIN's tell your teammates and the enemy what not to run into (walls, etc.) and ways to go around them. We have to mimic this through waypoints (unfortunately, a tedious process at times and extremely prone to breaking).
Getting the unlocked MED will give much more functionality. The original MED sucks compared to the unlocked one.
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