I am working with a customer that has many shared web servers and services. If we try to keep all the agent groups that would be touched during normal transaction flow in the same system profile, then we may have hundred of agent groups in a single profile. Note: this environment includes Apache, Java, Message Broker, CICS and IMS agents. Message Broker, CICS and IMS are the tiers which are shared by almost every application we are instrumenting. The client is very interested in seeing the complete PurePath for fault domain isolation. I know that usually we will see the complete PP in the transaction even when it crosses system profiles, but can we continue to count on that?
As well as a single system profile is recommended, therefore, should not be any top limit for the number of agent groups instead some management difficulties.
You can also review the below discussion which covered almost all the pros and cons about a single system profile.