Java is popular because of:
Platform independence
Sound object-oriented foundation
Functionally rich APIs available for the environment (e.g. EJB, Web Services, etc)
Some of the deployment issues you raise relate more to how some Java apps are developed moreso than there being issues with the Java "platform" itself. The fact you are still supporting Java 1.4 environments means you're having to support some really outdated Java environments and I would look to the Java application vendors as to why they rely on such outdated Java environments....
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