Hi V V ,
For the question you asked I will divide my answer in three parts.
As Universal messaging is a Software AG end to end messaging solution which support many protocols like JMS,AMQT,MQTT,LDAP,HTTP
and SoftwareAG (WM native Messaging).
And for IS to IS message transfer both JMS and native messaging are used but if you are taking about performance comparison then
JMS is getting little more points. however for IS to IS communication native messaging is recommended but JMS is also supported.
Our recommendations for the customers is to use WM messaging if dealing with Software AG Products. In care of IS is communicating
with third party servers or application like WebSphere, jBoss use JMS as it having open standard and there is no requirement of
webMethods knowledge for developers to integrate their application with UM .