Flatpak has annoyances like sometimes not following your icon theme, or just generally looking out of place because not picking up system defaults.
It works but I avoid it. On Arch Linux, there is a huge AUR repository where users have made native packages, and thats usually much better than Flatpak. But on Ubuntu, Flatpak is the only option sometimes.
For me its been almost 0%. :) Very happy with it.