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?
I just had to switch my work computer from Arch to Ubuntu becusse they want MDM on all computers now, and flatpaks are litetally the only reason i can tolerate it.
I now prioritise getting stuff from flatpaks, then the repos, and if they dont exist i use Distrobox to export any app thats only on the AUR for example.