The individual repo per mod thing sounds cleaner, though, I wonder how well it would work since that means you can only store the current version of the mod, no extra development files, etc, if you want that simple download link to work.
I definitely agree with forking similar factions. Magic and Tech both appear slightly differently in GAE's Magitech, Glest's Magitech, and MG's MegaPack. Not to mention FPM would also use them...
For the downloading though, it may end up necessary to use Git to store a "master copy" which can contain development files (blender, audacity, etc) and would make version handling easier, though to distribute the final project to everyone, you'd export and upload to another site, such as Mediafire (which you should not expect it to last on, all the more reason to have it also available on GitHub).
Unless there's any cleaner methods that don't require the user to have installed Git?