Package managers that integrate apt, flatpak, and (potentially) snap are a nice solution. Unfortunately, the one that happens to be on my system (Pop!_Shop) is awful.
Could you maybe elaborate, or link to more detailed criticism of Pop! Shop? I've also found that GNOME Software did a rather poor (though not that bad) job of exposing the multiple sources for a given package, but i believe this can be fixed with better UX (though i'm unaware of work being done in this space).
Pop!_Shop's UI frequently freezes when installing, searching, or even just opening an app's store page from the Gnome app menu. It also has some UI bugs, like the search bar being visible but un-interactable when on an app's page. It's definitely something that can be fixed with better UX. The actual selecting whether I want the apt version or flatpak version of a package works fine.
