My first thought: it would be cool if each mod had its own version history. This would help the modders access their older versions, which they likely don't have on their HDD (because frankly, who keeps 30 different versions?), and some users might also prefer some older version of a particular mod.
As I see it, each mod should have its own page with: synopsis, pics, download link and less pronounced links to older versions. And a comment section, using Disqus or a similar system.
Another thought: many mods are co-works, for example if they use graphics made by some other person than the one who wrote the ruleset. It would therefore be nice if we could do the same as
animemusicvideos.org, where more than one registered user can be listed as the author (and if you go to an author's profile, you'll see all the mods they participated in, not just ones they made themselves).
And yes, this means I want to be able to see all mods of a particular user by going to their profile.

Said animemusicvideos.org is an excellent exemple.
The system should also use tags, such as [weapon], [craft] etc. The system would be semi-flexible: when uploading, you choose one or several fixed tags, but you can also add your own if need be.
Anyway, it's a wonderful idea. I'll be happy to see this site done, and will gladly contribute!