Organizational Design

 I'm considering a departure from using Active Directory as the basis of "Organization" in my OIM system.   Presently, we use A/D - but it is oriented much  more to the needs of our windows environment  than it is to presenting the identities of our staff in some basis that resembles how the company and it's constituent parts are organized.  

Has anyone else departed from an A/D based org structure?  If you have what did you find the pitfalls to be?   Are there any benefits to be found?

Thanks,

Allen