Within System Center 2016, the 1606 version of Configuration Manager is included. Customers still on ConfigMgr 2012 (R2) can upgrade directly to 1606 now. No need to upgrade to 1511 (RTM) first and upgrade to 1606 afterwards.
|System Center 2016|
|Windows Server 2016|
Just download the bits and happy upgrade! :-)
Microsoft Hybrid Cloud (12-10):
Another big step in Hybrid Cloud – Windows Server 2016 general availability
Managing the software-defined datacenter with System Center 2016