I think option 2 or 3 would be the best. Let's give option 2 a shot and if worse comes to worse, go back to 3.
While the current setup is nice and allows for fantastic organization, it may be TOO organized (if that makes sense). That being said, I worry that option 2 may be create too much organization as well. How many root noobs are going to understand which option to choose as an example.