What are the functional differences between Windows Defender and Windows Intune Endpoint Protection and SCCM Endpoint Protection, apart from methods of management, if any?
(I am referring to the Windows 8 version of Windows Defender, which I understand to include the functionality of Windows Security Essentials)
Windows Defender pre-Windows 8 is a weak tool targeted at specific threats. It's not a full fledge AV, which is why Microsoft release Microsoft Security Essentials for home users. In Windows 8, Defender has MSE functionality rolled into it.
Endpoint for SCCM and Intune are functionally similar to MSE, except that it allows for more granular centralized management and reporting, which can be done either through Intune or SCCM. The SCCM and Intune versions are identical, except one is managed through a cloud-based Intune instance and one is managed through an on-prem SCCM instance.
So, basically, when talking about Windows 8 - all three are similar. It comes down to the management and reporting, or lack thereof.