Using Eclipse gets better as you get more comfortable with its peculiarities. I think the author did a good job of summing up the Eclipse experience--there's a lot to hate, and a lot to like. After using Eclipse for several years, it still has that "designed by committee" feel, but I do find myself missing some of its features when I'm using other environments.
I've actually been using the PHP... perspective?... for Eclipse and have found it to be pretty decent. (The author is right, some of the terminology is amusingly abstract.) Configuring the program just-so and learning to accept the slow boot-up are spot-on assessments.
That said, I should take some time to look for another IDE that captures the basic advantages of Eclipse. I'm mainly interested in having a panel with the project's directory structure, intelligent navigation (e.g. Ctrl-click on a function call to be taken to its definition in another class), and decent code completion and syntax checking. I might even be willing to pay for it.
