X11 2: Electric Bugaloo - The list of major graphical linux programs in active use is very finite and most of it doesn't talk to X directly but relies on stuff like Gnome or QT which are libraries that have frequent churn anyway. No?
I bet if you could get the Top 30 projects to target your clean shiny X replacement in one fell swoop you'll end up most of the way there in terms of adoption within a few years. Linux is command line centric and frequently updated after all with users who expect things to break anyway. "Old" X odds and ends that won't be updated can be thought of much like Java Applets are thought of now a days.
Oh you need that abandoned Chemistry application from 2006 that depends on X11? Spin up a VM. We can afford to be more pragmatic nowadays. Nobody expects to run 5 year old apps on their smartphones, but desktop linux can't afford a clean break once every 2 decades?