AppDynamics is not a replacement for the Systems Center Operations Management (SCOM) pack or a well-planned IBM Tivoli implementation, particularly when just interpreting PerfMon counters. SharePoint Server 2013 integrates well with SCOM, which is very useful but still optional.
Finally, AppDynamics is not meant to be a replacement for native monitoring tools but rather works together with tools from Microsoft and its robust partner ecosystem.