There are more reasons why to run applications as flatpaks. Someone wants to have the latest versions as soon as possible. For me as a user of Fedora which provides up-to-date versions of apps this is not a big motivation. Someone wants to run apps more securely. Again I usually trust software provided by Fedora and Flatpak sandbox is still not as strictly enforced as it should ideally be.
But where I really prefer using Flatpak to RPM packages are 3rd party applications. I’m usually running development versions of Fedora. Pre-releases on my work machine and Rawhide on my home laptop. They have been pretty stable for me, including applications in Fedora repositories. Unfortunately it’s not the case for 3rd party applications. Their authors usually don’t follow distro development closely and although many of them bundle as much as possible to avoid problems with changing dependencies, things break.
I used to use the Spotify client as a package from Negativo17 repos. But when I upgraded to F27, something broke and it stopped working. I’m pretty sure it was fixed later on after people started reporting it, but I didn’t want to stop using Spotify for the time being and didn’t have time to debug and report the issue. So I switched to Spotify flatpak and it has worked for me ever since.
The problem I had with very early stages of pre-released Fedora and Rawhide is that dependecies of GStreamer plugins in RPMFusion were usually broken. So I ended up without system multimedia codecs. It was often the case for VLC from the same repository, too. Then I switched to VLC and GNOME MPV flatpaks. Problem solved.
The last example is Telegram. Until recently I was using the official version. It’s not even provided as an RPM package. You have to download an archive, unpack its content to your home, run the binary which creates a desktop file… not very elegant in 2018, but once you do it, it just works. Well… until it doesn’t. I upgraded to F28 and Telegram suddenly took a lot of time to start up. It hung on some font config error until it timeouted and finally started. It easily took 1 minute. So I switched to Telegram flatpak as well. Works like a charm.
So what I really appreciate about Flatpak is that the apps don’t rely on the underlying system, so if the system changes e.g. due to upgrade to a newer major version apps don’t break. As I said it’s not such a major issue for distro-provided apps, but it’s certainly an issue for 3rd apps and Flatpak solved it for me.