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Depends. Most apps don't link against X, but the toolkits. If the toolkits can be modified to support a cleaner network protocol (something primarily vector based rather than bitmap based).

I don't think the parent poster is saying that X is related to GNOME and KDE's start menu clones, other than they both need changing.

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How cleaner? X11 is very extensible, if you wanted some vector graphics methods, you could just make an extension. Whole font drawing got replaced in this way, nobody really use old X core fonts anymore, everybody now uses client-based Xft system. (Well, yes, you could make a new version without this old stuff. But backwards compatibility and so.) In fact, this is what happens if you are drawing with OpenGL, you use X11 just to make a window to draw in, set some other stuff, handle input, but drawing itself completely sidesteps X11 and X server.

Are extensions negotiated over the network? So two hosts can decide they support a random high level primitive and just send that instead?

It's always client/server asymmetric communication. Server supports QueryExtension and ListExtensions commands. You can see extensions supported by your X server with xdpyinfo command.

(see www.x.org/releases/X11R7.5/doc/x11proto/proto.html specification for further details)

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