Eclipse has projects, what's the purpose of the Workspace that appears to group projects? Projects could live in the directory tree isn't that a more natural way of organizing different projects?
When you first start up Eclipse not knowing much about it, it feels like an unnecessary layer of bloat that new users have to get accustomed to first. You're forced to set up some organizing structure that, although specific to Eclipse, wants to live in the rather general-sounding place ~/Workspace.