Because Wayland pushes so much logic into the compositor, there's now the very real likelihood that things will work on Gnome but not KDE, or work in i3 but not Gnome.
Indeed. I wonder if these alternative tools are guaranteed to work no matter what compositor the user chooses for their computer. In X, the user has complete freedom over their WM and the tools will always work. You can build confidently on top of them. I'm concerned the same can't be said of Wayland.
This is why the org.freedesktop.* namespace exists. Very few people complain about org.freedesktop.Notifications not being portable. The next ones on track are org.freedesktop.Screenshot and org.freedesktop.Screencast.