There's discussions in progress about adding the ability to capture a single toplevel window to the screencopy protocol. Nobody's decided that it's a bad idea, it merely hasn't been implemented yet.
Regarding the fact that GNOME doesn't implement a lot of functionality: I don't think it's fair to criticise the protocol and architecture because one implementation decides not to implement a given feature. This is like saying "C sucks because some specific compiler doesn't support the feature I need". It's the compiler you've chosen that sucks in that case, not the language.
I'm sure there's some X server implementation out there that's also lacking features you want -- but you wouldn't blame the protocol itself for that implementation's shortcomings.
Regarding the fact that GNOME doesn't implement a lot of functionality: I don't think it's fair to criticise the protocol and architecture because one implementation decides not to implement a given feature. This is like saying "C sucks because some specific compiler doesn't support the feature I need". It's the compiler you've chosen that sucks in that case, not the language.
I'm sure there's some X server implementation out there that's also lacking features you want -- but you wouldn't blame the protocol itself for that implementation's shortcomings.