Emulating graphics hardware (GPU passthrough) with qemu is a pita.
You want to emulate Android apps, the best solution (Waydroid) only works on Wayland. Though this wouldn't be a problem if Xorg wasn't holding out. And Nvidia had played nice with Linux.
Memory and OOM situation management is a sham and another pita just waiting to bite. This could make you lose all your windows and in some cases even data as the solution involves forcing a reboot from your machine.
I could go on and on.
A lot of improvements have however been made in the usability aspect, main one being flatpak packages. But there's a terribly long road ahead to make Linux desktop feel less of a second-class citizen compared to other operating systems.