Currently the Microsoft templates are designed around Microsoft's best-practices. The base Windows Server template monitors a basic Windows well enough but when you throw another application on top of it sometimes those thresholds are no longer correct for the given application. For example Microsoft has their own guidelines on what are considered normal conditions for many of the counters which are also part of the Windows Server template but when the Exchange template is applied it would be nice if the Windows Server template was present the threshold values would be overridden to handle workload specific task.
