Many computer users have their appdata folder on a smaller SSD disk which would stop most users from using mods. The fact you will need multiple mods folder to use multiple incompatible mods will also be a problem since the main drives might be very limited in term of storage space. Modding the game rarely cause problem since you install the mods inside their own folder in the game directory, not like other games where the mod files go around loosely in all the game folder directory.
Please TFP don't do this