Ok, I changed my initial injection point to inject the session bean qualified with @MyDefault, and that fails, too. So, the problem is with the classes in my EJB #3 module, or my @MyDefault qualifier. Though, the definitions for both qualifiers are the same with the exception of the name. I double checked the final packaging, and everything seems ok. Each project's pom machine except for their specific artifact name. Their entries generated in application.xml match, and both are in the root of the final EAR package. I see no discernible differences between EJB module #1 & #2 with the exception of their artifact names.
It seems to me that it should work, but MyController needs to implement java.io.Serializable. What is the error you are seeing during the deployment? What is the EJB #3 module you are referring above? Can you post your exact EAR structure (what all is in each module) ?
I had the same problem. Adding manifest entries in the web application module fixed it for me.
The ear-subdeployments-isolated flag does not seem to work in Wildfly 8.1.