Ya Blackberry JDE needs a major overhaul. The GUI is out of date. The whole thing is crap. That is why i think in a few years if not less you will not see any major changes to the JDE. Which is why you see more and more plugins for thrid party IDEs. Next i expect to see a netbeans plugin.
Beyond that, to fix your problem for feature setups. You need to install the JDK 1.4 first and then install the JDK 5.0 or is it 6.0 now. Which ever.
ahh did not know about the 1.4 thing. But ya you have always been able to use netbeans but there was never a plugin for it. So all the little special specification and options that were not inputed through code could not be used. For example with the new eclipse plugin you can do everything within eclipse. and throw the crappy BB JDE out the window