XeTeX-generated PDFs are not compatible with the toolchains of some academic publishers (Cambridge University Press, which publishes the Journal of Functional Programming comes to mind, but I seem to recall Springer-Verlag having issues as well). Without full support for academic publishers, I believe that majority of TeX users could not upgrade.
Great question; I have no idea. We just get mail back from the editors that says things like, "your PDF breaks our scripts; regenerate it directly with LaTeX."
Some, like Springer-Verlag, also have an editorial process where you have to send your .tex files to them and they will merge all of the documents and run LaTeX on them. I don't even know how you could get xetex (or pdflatex) to work with that system.
