I firmly believe that the default values for EAR deployment (as defined in ear-deployer.xml) should be:
EAR Isolation: true CallByValue: false
The 4.0.4 GA installer at present bundles both of these values together into one check-box, and clearly there is an relationship between the two values. However, these values should be seperated out.
I think I can safely assert that the most common way JBoss is used is in an EAR isolated manner. Given that there is no way of an EAR application defining dependencies on another EAR application for use at deploy time - JBoss configuration should be supporting the most commonly used configuration out of the box - and that is isolated EARs with CallByReference optimisations enabled by default.