I'm not sure there is a universally applicable answer to this. Technology choices are really in the end an individual decision. I have used Java EE and EJB for many years now and have absolutely no regrets. I think it is an awesome technology. I've commented on Java EE/EJB adoption on other recent threads, please check it out.
Independent Consultant — Author, EJB 3 in Action — Expert Group Member, Java EE 6 and EJB 3.1
If your application does not need to worry about business logic, transaction management, threading management, security, and container managed components, then you may have a case for not using EJB but even in that case you can still use an EJB and not use most of those features
Java EE Evangelist — Author, EJB 3 in Action 2nd Edition — Java Community Process Member
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