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.
They can have positions lf existing windows saved and restored (still rolling out), and I think can ask for some details of initial placement outside of that too.
Of course still very limited and not handling the specific cases you mentioned.
Setting up hotkeys is possible, just in a very different way. You have to have the desktop environment forward it, and for now specifics differ from de to de. Generally they can all bind actions though. A safe minimum-viable way should be to add shortcuttable actions to the desktop file I think, though the qt shortcut stuff should also generally work I think.
kwin at least has had that for a while
Personally for me I used to have a script invoked by tilting the sceoll wheel that’d send a shortcut (e.g. ctrl+page-up/down) to the window under the cursor without focussing it, letting me change tabs of unfocussed windows.
I think I did that by quickly changing input focus, sending it, then changing it back, with xdotool etc…
On wayland I’ve tried implementing that via kwin scripting a few times, but found it so hard to debug and to work with in comparison I never managed to recreate that simple tool.
Having universal posix-like tools to affect the window manager and user input from console is definitely something I miss occasionally.
Largely this is just a lack of wayland tools I am sure. And I must admit it’s been a while since I last tried.