I fully switched to Linux in 2024, my last desktop Linux experience before that being at least five years prior.

• Windows behaves a bit more gracefully then Linux when the VRAM is being exhausted. On Linux I can get graphics artifacts and sometimes Steam crashing. That mainly becomes relevant when doing GPGPU stuff, though; gaming works fine.
• Some apps use GTK4. Since GTK3, GNOME has been moving away from a "regular" desktop experience and towards this weird pseudo-mobile thing that goes against all established conventions. That might be nice if you really like their style and use nothing but GNOME, but it's really annoying if you don't. I long for the good old days where action buttons weren't crammed into title bars.
• Occasionally having to manually fix package updates. Only an issue because my distro is Arch-based and that kind of stuff is to be expected there.
• I haven't managed to get three-finger swipe mapped to PgUp/PgDn so far but I use the trackpad rarely enough that I haven't bothered investing time into it yet.
• Occasionally the system just shits itself when rapidly switching between different users' desktop sessions. Again, that happens so rarely that I haven't bothered trying to deal with it yet.

On the other hand, I'm happier than expected with Wayland and PipeWire. They just work with little fuss. Sure, I'm a KDE user and Wayland is reportedly less fun outside the big DEs, but for me it just works.