I think the main complaint about using a protocol like RDP or VNC is that they require the remote side to manage an entire desktop. When I run an X11 application remotely, it opens a window on my desktop rather than a whole other desktop. This becomes even more pronounced if I want to run multiple applications each running from a different remote host. The X11 way integrates more naturally into my workspace. Now, if RDP or VNC can be made to work with individual windows rather than entire desktop (maybe it already can, I don't know), this would change the game entirely.