not sure if anyone has moved from this or not but there is a much easier way to sysprep then going through and removing the native apps. All I did was do a fresh install and have the OS offline. Go to services and disable Windows Update. Then go ahead and put it back online, install all my apps and use the SCCM 2012R2 capture ISO. Worked like a charm. It’s something in the Native App updates that kills sysprep.