Aside from philosophical issues my experience with Flatpak has been excellent. There’s some theming steps you need to do to make them feel like regular apps, which I feel is clunky design. No Flatpak-induced instability from what I can tell. Setting up directory permissions is sometimes slightly annoying but Flatseal makes it trivial, and most Flatpak permissions are set up properly out of the box these days.
I haven’t noticed any start-time delays when launching Flatpaks as opposed to regular apps - I don’t know if they’ve fixed that or if my system is just too powerful. The only app that I’ve personally noticed is weird is VSCodium, which has trouble escalating to admin permissions when you’re trying to edit privileged files. I still use the regular version for that reason.