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?
Really awesome. They're all contained within my home directory too, so when I swap distros I can just copy my home dir and all my installed apps are carried over that way. Super useful feature that never gets mentioned! The downside to flatpaks is having to use them for cli in any way is a huge pain.
Why not use a seperate /home partition if that's something you value?
I do, that doesn't keep packages installed between distro reinstalls or swapping between entirely different distros. I'm talking about the actual packages and app data themselves that are contained in home.
For automatic installation I recommend ansible, its real easy
There's literally no need. It's auto installed because everything is portable and most applications that launch .desktop files know to look for it's directory.
Then you didn't explain it very well. Your former comment clearly states that copying the files keeps the packages (so you don't have to redownload?) and the data, but "doesn't keep packages installed" (hinting that .desktop files don't get found)