Hello,
I see this post is a bit old but was hoping I could get some help as I am having the same issue. I am running WSUS on a Windows Server 2012 R2 and its version shows 6.0.xxx. I am installing SCCM current branch and it keeps saying that the WSUS version needs to be at least WSUS 3.0 SP2 or later. But it should be since it is version 6.0.xxx. I did notice my WSUS server was configured on WID, would that cause any issues?