Currently at this point in time you will be unable to monitor your Exchange 2010 environments via SCOM R2. If you install the MP you will come across the below errors and if you go install the required KB you will hit a problem as this update has not current been released.

“Critical hotfixes required for reliable operation of the Exchange Server 2010 and other management packs are not installed on this server. Please see the appropriate KB article for more information, and to download the required hotfix.

For Operations Manager 2007 SP1, install KB 971541 (http://go.microsoft.com/fwlink/?LinkID=167911)

For Operations Manager 2007 R2, install KB 974144 (http://go.microsoft.com/fwlink/?LinkID=167912 “ 

This is Due to the KB update for SCOM R2 currently not being released, so for the time being you will not be able to monitor your Exchange 2010 environments via SCOM R2.

After speaking to Microsoft the KB should be released before the new year.

Thank You

Daniel Davies