Hi,
Feature data sets are not folders. Using them for organization will add administrative limitations, especially when it comes to permissions.
For data in a feature data set:
Read/Editing permissions are all or nothing. No granularity.
Register as versioned are all or nothing. No granularity.
If one feature class is opened in a fds, they are all "locked" from an administrative perspective.
Feature data sets should only be used for data that will participate in geometric networks,topologies, etc.
If you want to organize your data for users I'd suggest using layer files and folders.
Good luck!
Anthony