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?
There's a pretty simple reason. It's that developers don't have to spend the time to package for every single distro. I know I wouldn't, I'd just focus on packaging for the distro that I use and flatpak. Having flatpak also means that some less known distros start with a big amount of apps available from the get go with flatpak.