The embedded Glassfish is provided as huge uber jar. But wouldn't it be possible to provide it as POM with all required dependencies? This approach would allow to avoid dependency problems as I am facing them now. Sometimes the version of classes contained in embedded Glassfish differ from the dependecies required or provided by other libraries.
SLF4J, ASM, and Joda time are some examples. The POM approach would at least allow to analyse the dependencies of embedded Glassfish and to exclude some dependencies if the collide with other dependencies.