I just had a cool idea and I googled it and looked for it in bugzilla but I haven't found anything. My idea is this: that portage packages could be tagged or labelled rather than placed into categories. Each ebuild package could have any number of tags. There would be one directory where all the package directories would be stored in a flat hierarchy and the category directories would now be tag directories. Inside the tag directories would be symlinks to package directories. The advantage of this is you could then do interesting searches a packages with a certain combination of tags. I suggest to go along with this, that all ebuilds have a unique name.
Uh... please, take this to gentoo-portage-dev mailing list once you've consider all implications. And, flat namespace plain sucks.