My totally unscientific opinion (with a double-your-money-back guarantee!):
I’m not crazy about either Flatpak or Snap for that matter as there’s so much backend baggage for both as well as certain hurdles regarding privileges and access to the file system (somebody please correct me if I’m wrong or working with dated information.)
My other completely prejudiced, unfounded bias against Flatpak is that it appears to have been adopted by RedHat as “the one true way,” and what with IBM’s/RedHat’s behaviour anti-FOSS behaviour lately, plus I’ve almost always have been an apt user, I find it a pill hard to swallow.
Me, say what you will about the security issues and its other flaws, but I like AppImage.