I find it interesting that just about every support request is how to configure the permissions.
I shouldn't have done what I did with them, but I dunno, I couldn't think of anything that actually worked better... and in the two years since I wrote it, I still can't think of anything better to do the job that did.
But I feel bad for all the support issues because people don't understand it :(
You did a great job! Had we had time to bring along a FUP version or two I think it would have smoothed it all out.
Permissions are a complex thing to do. Don't think you could have done worse (ha) or better (ha).
The only issue I see with how permissions are done in SD is that user are used to how SMF does it by the time they get to SD so they are expecting similar. We never did get around to documenting SD for public use so the support questions well just makes sense. The permissions are certainly a new approach and without an FAQ of sorts I'm actually shocked that there hasn't been more support topics than I've seen.
Also note that usually once a user grasps the concept of dealing with the roles/permissions/departments thats pretty much it. Effectively I say there is nothing wrong with this approach to permissions and the issue is more the lack of documentation for 2.0.