• no OS level components
• duplicate libraries as some core apps (editor, filemanager, Desktop) cannot be flatpaks (yet?)
• old runtimes etc. dont force developers to keep them updated. Often thats because or 3rd party packagers though
• complicated packaging, I heard that the Flatpak builder is better for certain languages.
• theming issues I heard (on Fedora Kinoite Wayland it just works, and I can also force themes per app)
• bad permissions by default (best we have though)
• bad run commands (this could easily be fixed, and I have a script for it)

For OS components / packaging every part, Snaps may work, but for GUI apps they seem subpar and nobody really cares.

Nix may be way better for installing just anything compartimentalized, but there is no permission system (thats why packaging is easier).

But Flatpaks are really great overall, Bubblewrap, KDE Settings / Flatseal, Portals, official app support. Its really really important.