Windows Update problems on new Windows Server 2012 (R2) machines are fairly common.
Common advice is to clear: C:\Windows\SoftwareDistribution
This usually works, but unfortunately it also resets parts of the Windows Update history.
In some cases it’s not necessary to clear the SoftwareDistribution folder.
If Windows Update is stuck at Preparing to install for a long time (hours), the problem may be resolved simply by restarting the Windows Update service.
From an elevated command prompt run:
net stop wuauserv
Usually the Windows Update service will be started automatically.
In case it isn’t, start it with:
net start wuauserv
This simple procedure solved the Windows Update problem I experienced today. Afterwards it was no longer stuck, but installed updates normally.