When I create a web application and use Tomcat, I get a better user experience when I subsequently attempt to profile 
that application than when I use GlassFish.

According to the profiler team, this is because the Tomcat plugin reports the JDK version that is being used to run 
Tomcat.  The GlassFish plugin apparently does not do this.  So the profiler user interface has to pop up a dialog on my 
first attempt to profile that says: "The Java platform for this project does not support profiling.  Do you want to use 
one of the Java platforms listed below." Or some such wording. :-)

Bottom line: it is minor, but a bit of a nuisance and easy enough to fix from the profiler user interface perspective.  
But not until the GlassFish plugin provides the information that is needed.