Sounds awesome! Can't wait to try this out. A couple quick questions:
-Mission scripts: Include GML script into the mission so that you can completely customize the mission with GML. GML is Game Maker's built in scripting language so you'll be able to do anything I did with the missions
Do you plan to include a sample mission or two? I'm not too familiar with GML, but I bet I'd be able to pick it up pretty quick with a couple completed missions to look at.
The baseline functionality for the Encounter Maker will allow you to import a bunch of custom ships and place them on the map. This will then be saved into a self-contained encounter file (which will have all of the .shp files required stuffed inside).
So, will loading one of these wipe anything already on the map (read: is it an entire saved map?), or will it just lay whatever's in the file on top of the existing map? Basically, could I use this to spawn formations of ships similar to the spawn formation feature in the sandbox?