Mods should all be in a single mod folder. Mod bundles should contain an XML file in the root of the bundle with the mods name, version, author and other pertinent info. The game should load all mod bundles "config.xml" file letting you choose in game which mods to enable. Enabled mods should be in a second list of active mods and allow you to adjust each mods priority. Mods with a higher priority would override same modded files from other lower rights mods. Ofcourse if a lower mod requires a file modded and a high ranked mod undoes its modification, it can break the game, but there you have incompatible mods. When playing multiplayer only mods that are enabled on the server should be loaded...
Oh, autodownload of missing server mods and HTTP redirct would be a bonus.