Support for Windows Server 2016 as a guest system is added in Hotfix 1 for Update Rollup 11 of System Center 2012 R2 Virtual Machine Manager

Microsoft Support still gets frequent inquiries about whether System Center 2012 R2 VMM can support guests running Windows Server 2016. Installing  Hotfix 1 for Update Rollup 11 of Microsoft System Center 2012 R2 Virtual Machine Manager (VMM) enables you to create Windows Server 2016-based guest virtual machines (VM) in VMM.

Help article 3199246 contains the link to Hotfix 1 for Update Rollup 11 of Microsoft System Center 2012 R2 Virtual Machine Manager (VMM). This hotfix contains two update packages for Update Rollup 11: One for the VMM Server and the other for the Administrator Console.
After you apply this hotfix, you can create Windows Server 2016-based guest virtual machines (VM) in VMM. This hotfix also enables you to select roles and features that are applicable to Windows Server 2016 when you create a VM Template.
Note: To apply this hotfix, you must be using Update Rollup 11 for System Center 2012 R2 Virtual Machine Manager.