Full Permissions are able to be set right down to the data row level.
Easy to use interface to manage users, groups, permissions.
Extract Status pages easy to use
Ability to customize menus
Ability to embed dashboards into other applications
Ability to edit Dashboards from Tableau Server Interface (with sufficient permissions)
Ability to manage extracts/datasources from server interface
In built troubleshooting
Ability to create "sites"
There are still issues with displaying dashboards with lots of data (despite what tableau show off at Tableau Conferences)
Could there be better extract interaction between Tableau Desktop and Server?
Make sure you have fully specified machines running your Tableau Server Instance
With regards to permissions it is best to set all your users to be Publishers then create a series of groups with names corresponding to the level of permissions that you wish to apply to your users.
Add your users into the various groups appropriately.
Apply groups to each project to apply permissions.