MyEclipse is much more robust, has more features, it stable and allows for a much more flexible project layout. I’ve only used Lomboz a small amount, but a quick example of the features MyEclipse has that Lomboz doesn’t is that MyEclipse supports JSP code completion and error marking, JSP expression language support, XML completion, Struts wizards and tooling, Web application debugging (I don’t know if Lomboz has this), XDoclet support, HTML code completion and error marking and application server deployment tools.
I’m not part of the original MyEclipse team, and the reason I ever found this project was because I was using the Lomboz plugin and really not getting any of the features I needed.