I used to always remove Fedora Flatpaks, but I've grown to like them.
They are built from Fedora RPMs, so follow Fedora's packaging and building guidelines. Meanwhile Flathub and snap are the wild west of packaging; many flatpaks/snaps are just repackagings of existing packages, which are often built against ancient glibc and libraries for broad compatibility for traditional packages.
They use libraries that are in Fedora's repos. So any vendored dependencies in a Fedora Flatpak will get automatically updated once the app is rebuilt. Meanwhile on Flathub/snap, those vendored dependencies need to be manually updated (though there are tools/bots for Flathub that automatically check for updates and can even create merge requests). Upstream app developers may not upgrade their apps in a timely fashion.
I also much prefer how Fedora handles runtimes. I only have two Fedora runtimes on my system, Fedora Platform and Fedora KDE 6 Platform, which are both based on Fedora 41. Meanwhile on Flathub, I have 52 runtimes installed. Thankfully most of these are small, but there are still quite a few larges ones. Multiple versions of mesa, multiple versions of Qt, multiple versions of the Freedesktop runtime.
By far the biggest disadvantage is that they're affected by Fedora's copyright/patent restrictions. So most multimedia apps I end up installing from Flathub so I have working codecs. But there is some work being done that would allow Fedora Flatpaks utilize ffmpeg-full from Flathub.