I still have weird glitches where applications don't seem to update on screen (chrome and firefox, both natively doing wayland).

Lack of any solution for programmatic geometry interaction. This one has been afflicted with 'perfect is enemy of good', as the X way of allowing manual coordinates be specified is seen as potentially too limiting (reconciling geometry with scaling, non-traditional displays), so they do nothing instead of proposing an alternative.

The different security choices also curtail functionality. Great, better security for input, uh oh, less flexibility in input solutions. The 'share your screen' was a mess for a long time (and might be for some others still). Good the share your screen has a better security model, but frustrating when it happened.

Inconsistent experience between Wayland implementations. Since Wayland is a reference rather than a singular server, Plasma, Gnome, and others can act a little different. Like one supporting server side decorations and another being so philosophically opposed to the concept that they refuse to cater to it. While a compositing window manager effectively owned much of the hard work even in X, the X behavior between compositors were fairly consistent.

I've been using Plasma as a Wayland compositor after many failed attempts, and it still has papercuts.