Microsoft just recently released a preview pack of a management pack that can be used to monitor Windows Server 2012 R2, good job Microsoft! 
You can download the preview pack here –> http://www.microsoft.com/en-us/download/details.aspx?id=39375
The management pack includes monitors for most of the Windows Server features. Including some awesome feature for Hyper-v 2012 R2, including for instance Host Health Dashboard and Virtual Network Usage.
It also includes for other features such as Cluster, AD, ADCS, RDS, and even Server Essentials.
Now Microsoft should hurry up and release some management packs for System Center 2012 R2 as well that would be great!