: Does anyone have any recommendations on some kind of version control system
: that would be amenable to a Marathon scenario project?
For the map file and images, set up a git repo with the unmerged stuff in Atque's folder setup. Git can handle all those files just fine: levels, physics, scripts, terminals, picts, shapes patches.
The generated replacement textures shouldn't be a problem either: we store all the XBLA shapes in Subversion, and git is not that much worse than SVN. You might have to pay if you want a repository bigger than 1 GB.
It's the source files for the graphics and music that become an issue. Maybe all you can do for those is upload them or share them on dropbox. You (or someone) will probably have to do at least a little maintenance in order for distributed development to continue at that level.