One thing I really dislike with snap/flatpak is how it breaks connectivity with other parts your system. Example, I run Ubuntu and wanted to use a smartcard for authentication in certain websites. That didn't work because Firefox is in a snap, and can not communicate with the pkcs11 libraries... To solve that I have to scrap Firefox as snap and install as debian package from PPA.
In an ideal world, the application would be Flatpak or Snapcraft aware (or there'd be a middleware to intercept these calls), and ask for access to parts of the system it needs.