I've been involved with Linux for a long time, and Flatpak almost seems too good to be true:
Just install any app on any distro, isolated from the base system and with granular rights management. I've just set up my first flatpak-centric system and didn't notice any issues with it at all, apart from a 1-second waiting time before an app is launched.
What's your long-term experience?
Notice any annoying bugs or instabilities? Do apps crash a lot? Disappear from Flathub or are unmaintained? Do you often have issues with apps that don't integrate well with your native system? Are important apps missing?
Same. In addition to the prompt-based permissions that @Kusimulkku@lemm.ee brings up, I'd like to see more granular control of permissions. For example, a flatpak app's access to webcams, controllers, etc. are all controlled through just one permission:
--device=all
(aka "Device Access" in KDE's Flatpak Permission Settings).