The biggest thing I can think of is that X11 is more flexible when it comes to specifying custom resolutions; which some people use to output 240p on CRT TVs for emulation. AFAIK, there is currently no real equivalent for xrandr on any Wayland compositor.
I’ve also noticed that Grsync’s password prompt is broken on Wayland. Thankfully, it has a feature that lets you preview the command it’s about to run, so that you can copy and paste it into a terminal.
Being a KDE user on EndeavourOS, I use Wayland everyday. I switched over a few years ago for Waydroid, but now X11 isn’t even an option for me with the current release of KDE.
My personal bugbear is that there is no compositor-agnostic way to tell what workspace a window is located on. This means that taskbars cannot implement an “only show windows on the current workspace” setting, which frustrates me to no end. (Taskbars like the LXQt and XFCE panels still have the setting, but it does nothing.) There is not even any proposed protocol to support this, and acceptance and implementation would take years even if there were.
Integrated desktops like KDE probably roll their own custom implementation, but out in Labwc land I’m shit out of luck. (1 2 3 4)
Reading those issues… WTF? How many alternative implementation of basic functionalities are there? I think I remember reading back in the day that this will be the issue with Wayland, every DE will have to implement way more than with X. Now I understand what they were talking about.