Questionable design choices

Atomic Desktop doesn't have an update indicator tray icon

The update is being queued automatically but there isn't any indication of this anywhere aside from calling rpm-ostree status.

This might be a ublue issue, as from what I can tell I don't think the base Fedora Atomic Desktop even includes automatic updates.

ostree image selection on grub menu just lists numbers and doesn't give any details about what each pinned entry means

This is silly. Knowing what the various boot options mean is useful, just printing numbers doesn't give any helpful information unless you already know what they are.

Multi-monitor panel handling

When using multiple monitors, KDE forces you to create a separate set of panels for each monitor. While you can clone the panels between monitors (which makes a duplicate), there is no way to make the same panels appear on all monitors.

The consequence of this is that after setting up the taskbar and start menu on monitor A, then cloning them to monitor B, any change you make to the panels on monitor A doesn't apply to B.

The start menu (application launcher) is quite annoying for this, as it doesn't persist the height of the start menu OR the favourites order between monitors. You want to add a new favourite to the start menu and have it in the top left? Make sure you do it on every screen as moving it only affects the copy of the start menu on the screen you moved it on! (although the favourited items do get synced between monitors... just not their order)

Program volume not alterable when program isn't playing sound

If a program isn't currently outputting sound the volume control for that program disappears out of the volume control, preventing you from being able to customize that program's volume. This is quite annoying e.g. for games where the audio stops playing when the window loses focus; you can't control their volume at all.

No trash for /opt

/opt doesn't allow you to send things to trash.