Recently, I provisioned a brand new Dynamics 365 for Operations Environment with Update 3 (November 2016 update) + patched it up with KB 3215650 - this is the KB which enables the mobile workspaces that are provided in your Microsoft Dynamics 365 for Operations.
Unable to see the Mobile App Option under System Administration - System Parameters. Did some troubleshooting like restarting the AOS Service but with no luck
After some troubleshooting, I went to Visual Studio, opened up the object class SystemParameters_SCMMobileExtension which does the job of adding the mobile option. I explicitly did a build and synchronize for this object and then voila! :)