I see many people wanting that, but realistically, will it happen?
take chromium browsers for example: their flatpak versions replace the regular chromium sandbox, which is not good. for most people, browsers are the most important thing in the entire OS.
flathub is planning to add paid software support, which on another hand would be great, as linux lack paid stuff.
the most used desktop distro is ubuntu, so most linux users don't really need to rely on flatpak (since ubuntu have support for everything), which means flatpak needs more advantages over regular system packages, rather than just being avaliable on most distros.
IMO, what will happen: paid software will completely rely on flathub, browsers will still mainly be used though system packages, and the rest will be mainly flatpak as well, if flatpak team keeps investing on making their "package manager" better.
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