Well it doesn't help that the game wasn't developed with modding in mind, unlike Skyrim where the game natively supports it.
That being said though, I think GTAV is quite flexible since it allows adding/replacing assets through DLC packages.
You can leave vanilla files untouched (with the exception of update.rpf) and keep things organized.
Rockstar most likely made the game this way to make updating easier, and that can be used to our advantage.
I don't think this was possible in the past series without the use of third-party tools.
