eh, I duno. kinda depends on your organaztion I guess. for me, instead of clicking on a source tab I have to double click a .java file instead. but it's not like my source files are all over the harddrive.
for production purposes I have in the past used an IDE for the coding but.. I've never used a WYSIWYG IDE for anything, though.. [unless you count Flash. but heh]
WYSIWYG editors, yeah... brr.
but even if you have everything in one place, you still have packages and crap you have to walk trough.
offcourse next to that you have code completion, refoactoring, debugging and as you mentioned profiling.
wat's not easy to use about eclipse, sure finding decent plugins is a f-cking mess
one time i tried to use it i just did not get it i gusse it depends what your used to i could not figure out Sun java studio creater ever