I'm glad the author of MedModManager sees the value in a tool like this! We may find it useful to swap notes.

There are actually more uses to an installer/uninstaller/launcher. In a perfect world, the -mod:<folder> switch would be sufficient to launch any mod, and they would never conflict with each other. However, the truth is that modders are ever more demanding of the features they want to add to their mods, and ultimately discover that in order to implement some of them that they need to go outside of their "assigned directory" and make changes or additions elsewhere. I can show you an example in almost every mod I've downloaded, which is about all of the major ones. An installer with a built-in version control system can keep track of which mods have modified/added which files in which order, allowing it to restore the application to any previous condition after performing an installation. The launcher could use information provided by the installer to eliminate the performance problems that some modders (like the guys who wrote "Rise of Persia") complain about when using the -mod switch.

Of course, the other major advantage is that it will make it extremely simple for modders to create their deployment packages. They won't have to worry about things like duplicate file names ("readme.txt") or file structures. WinZip has the capability of warning about overwriting files, but once again you're placing the burden on the end-user.