Many don't like eclipse at first. I think it's really a personality thing, but it also depends on what kind of work you're doing.
If you're writing core Java, like a library or something, a text editor ought to do. You could also try IntelliJ community edition.
If you're doing JEE, Spring, OSGi, or mobile stuff, you'll actually want a true IDE. Don't think it's unclean to use one. Consider the IDE part of your toolchain. It's not so much the code completion and syntax highlighting as it is management of deployment descriptors, artifact formats, configuration management, and integrated build and deploy functionality.
If you want to get started with good, out-of-the-box functionality, go with NetBeans. It feels very integrated (that's the I, right?) and it has project templates with sane structures for almost every type of application you're going to build.
Eclipse has similar templates, but it's more of starting point that requires customization to really get rolling.
If you're new, see how NetBeans feels. Later down the line, when you're more comfortable with all of the internals of how JEE works, I'd recommend going back to Eclipse and looking at it with your new knowledge. Things will make a little more sense.
