Funny, for me it’s the opposite. To me, it makes more sense to use Java when coding agents, web-services et al. But I’m mainly doing web-development, and very seldom traditional notes stuff. Java feels like a more “complete” and more suitable toolbox for that purpose (web, xml and networking stuff).
I like the “new” Java editor a lot (it’s a huge improvement!), but the double-save-trouble is very painful, and not at all intuitive. A big #fail imho.