I always use Flatpaks when available, I have been using it for about 1~2 years and honestly, I haven’t found any issues that are deal breakers, mostly some missing storage permissions, but KDE makes this easy to deal with. I know some apps have some issues, but the biggest one that I had is that Steam Flatpak still requires Steam-Devices to be installed as a package, but that’s more to do with the way Steam Input works.
The only issue that I have is that uninstalling Flatpaks should present an option to delete the app data.