Not all mods are created with a standard rule of compressing an archive. Some people who make the mod do not even understand how the compressor works. As long as all the required files are included creating the proper directory structure should not be difficult.
Here is what the directory structure should look like.

This shows the folder in a folder bad installation. The game will still find "My Mod" but does not have any of the files in the proper directory.

Another bad install and here the game will show mods like "GameInfo", Mesh etc.
