My home directory is a lot cleaner, dependency issues are a thing of the past, it’s easier on the developers, I’m getting updates faster (not having to rely on distro maintainers), my installs are more portable than before.
I wish we had Android-like permission setting, where it pops up asking if each program can use X permission as it requests it.
And I wish Gnome settings would implement some of the more basic flatseal options (flatseal can still exist for power users), although that one isn’t a shortcoming of flatpaks itself, it’s more to do with development manpower on the Gnome side.
Overall I’m really glad that one of the biggest annoyances in Linux is getting resolved. We’ve finally pretty much agreed on an app distribution and packaging standard