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.
Correct me if this is no longer the case, but:
Starting an old game fullscreen and having the lower resolution fill the HD/4K or what have you display and not just display a small box at 1:1 ratio with black borders all around. (Might also be AMD-related, not sure? X can do it, though.)
Allow custom key maps with multiple level modifiers that are unconditionally accepted system-wide and not just in all applications except for that one that just won’t take that key combination.