Gnome 2.22.2 can not be built without gnome-extra/swfdec-gnome gnome-extra/swfdec-gnome depends on media-libs/swfdec media-libs/swfdec must have the gtk use flag to be used by swfdec-gnome 1: If gnome can't be built without the swfdec, shouldn't it be in gnome-base and not gnome-extra? 2: "gtk" is a global flag. Having "-gtk" in /etc/make.conf should be possible. Quite frankly, I'd like to see a way to build gnome without swfdec-gnome. It's not useful on a headless server where all clients use remote X.
swfdec-gnome is in the gnome meta because it's part of the gnome desktop as upstream intend it. The classification in categories in gentoo is not so tied to upstream intent and since a gnome desktop can run perfectly fine without swfdec-gnome and it ended up in extra. If you don't like the dependency in the gnome ebuild I'm sorry but you'll have to either maintain your own ebuild in an overlay or use gnome-light. Hopefull, when portage 2.2 lands, you'll be able to create your own "gnome" set which will only include what you want and be easier to maintain.