There are two known compatibility issues between Enterprise Server 2.1 and Java ES 5 (JES5).
The JES5 Service Registry is not compatible with Enterprise Server 2.1 because of the JSF 1.2 version provided by Enterprise Server 2.1. The Service Registry needs to be upgraded to JES5u1 prior the Enterprise Server upgrade to 2.1. This limitation is also documented in the Service Registry documentation.
The JES5 Portal Server is not compatible with Enterprise Server 2.1 because of the JSF 1.2 version provided by Enterprise Server 2.1. Portal Server needs to be upgraded to JES5u1 prior the 2.1 upgrade to 2.1.
On a Java ES 5 setup that has Portal Server on Enterprise Server 8.2, upgrading Enterprise Server 8.2 to 2.1 makes the Portal Server unusable. Enterprise Server 2.1 uses JSF 1.2, but the JSF-Portlet bridge in Release 5 Portal Server does not support JSF 1.2. On Solaris/Linux the Portal Server needs to be upgraded to JavaES5 Update 1. On Windows do not upgrade Enterprise Server to 2.1 if you want to continue using the Release 5 Portal Server, as Portal Server is not supported in Java ES 5 Update 1 on Windows.