One big difference with POSIX/UNIX is the lack of multiple users. My understanding is Haiku is working to add support for multi-user/privilege separation of some kind, but at least for BeOS this was a fairly big difference.
What isn't properly supported yet is running GUI applications as anything other than UID 0. Adding support for that will require some careful refactoring across a few different components. Actually, if you added a handful of hacks in a few places it might work already...