To me, those aren’t real Flatpak issues. Yeah the CLI interface is clunky, but why would I care when the XDG desktop file path is being added automatically and Flatpak is for desktop apps, not for CLI. It only matters when debugging broken application, but at the same time it’s not that hard. Overall that also gives us ability to have multiple instances of the same app installed multiple times from different sources.
Flatpak can easily work on anything that has it in its repo and usually the setup is piece of cake. I had much worse time dealing with some AppImages due to its wild guesses about what the host system is, like libfuse version. Desktop integration is really meh imho and I could never figure out how to use it effectively without some lost desktop files here and there I had to clean manually (haven’t tried in a couple of years now, it could be better now).
Wayland support is intentionally broken by AppImage creator/maintainer just to be able to point finger at Wayland ecosystem and say: look - unfixable. Lately the same dude wanted to propose collection of out-of-tree Wayland protocols to make it more like X11, which is horrible idea and no actual Xorg/Wayland dev would have any interest in doing, because it defeats the decade long efforts to change how the graphics stack works.
AppImage maintainers also showed their disappointing attitude when trying to get OBS to use it, assuming everyone will be interested in having that package format published on official projects website, while conforming to all requirements and doing the work of adjusting app to that format. To no surprise, OBS was horribly broken when built that way, and they demanded OBS devs to fix it, not getting how could they possibly not be interested in having app image, while already having well built (I use it myself, it’s great) Flatpak package.
Flatpak does sandboxing with fine tuning abilities (using something like Flatseal or new KDE’s built-in KCM) + there is actual verification process at least for new apps on Flathub. I don’t say it’s 100% safe, but compare that to AppImages which is just running randomly downloaded binaries from the web with full filesystem access.