It’s only really an option for GUI applications which I intend to launch from a GUI which is a real turn-off as a long-time CLI user. I often want to run something like gimp file.ext from the CLI but can’t (easily) with a flatpak.
I also find the permission system gets in the way quite frequently as well. Like I was using some graphics program from a flatpak (I forget which - rawtherapee or maybe digikam) and it could only see certain directories. I get the security restrictions but it was a bit of hoop-jumping to try to figure out how to get that to stop, and in the end I just installed the snap…