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.
Automated window positioning through tools like wmctrl and xdotool. There are replacements on Wayland but they’re either missing features or are tied to a specific window manager.
I use Xfce, and I like writing bash scripts that can work anywhere.