Storage space mostly isn’t as bad as it is with AppImages. Each AppImage stores all the libraries it needs, even if they are shared with another one. They can’t even know if they have shared libraries. A single AppImage will probably actually use less storage than a single Flatpak if you only have one, just because the AppImage only uses exactly the libraries it needs, while Flatpaks use shared sets of them. That being said, Flatpaks generally get less bad the more of them you use, because of the shared libraries. They’re still a whole extra set of libraries on top of your system ones though, plus they put out a new set every year. Apps that are still under active development generally get updated to the latest version, but older apps that are basically finished often require older libraries, so that’s more space used. Overall for a one off program when you’re not using universal packaging systems regularly AppImages are mostly better, but if you’re going to be using them regularly Flatpak quickly becomes far better. It still uses more storage space than just using native apps though.

Another difference between Flatpak and AppImage is that it can be kind of a pain to theme Flatpaks to match the rest of your system, and I don’t know of any good way to do it with qt6 apps yet, but it’s just straight up impossible to theme AppImages. They can technically have themes built into them, but unless you’re using Adwaita, or maybe Breeze if you’re lucky, they just don’t, and having to rebuild your own custom AppImage completely defeats the main benefit of using AppImages.