If you're going to build a modding system into your game, please make sure you are familiar with the chain of responsibility pattern. Modders should not be overwriting assets in your game folder if they want to reskin something; they should be giving you a handler that redirects requests for the original assets to the replaced assets. That way the mod can be removed, have its priority changed relative to other mods, etc etc, without having to screw around recovering assets from the source media.

Imagine if every aspect of a game - every location, every weapon, every character - were developed as a mod for an empty/vanilla base? And I mean using the full modding mechanism that is eventually released to the gaming public - with an ability to mix and match everything. When releasing, you compile all your mods together into one big one. I think the result would be interesting.