Because there are pros and cons for each type of packaging but native distro packages and Flatpak will go-exist. It does already on my machine.
Distribution packages:
+ necessary for base system
+ small memory requirement
+ small package size
+ all checked by distro
+ work well together
+ on fix, fixes it for all
o lot of work for maintainers downstream
- bugs hard to figure out for upstream
- problematic with closed-source
Flatpak:
+ programmer packages is/her software once and only once
+ support all distributions i.e. Linux
+ use selected dependencies
+ control-groups and namespace are in place for lock-in
+ autonomous offline package handling e.g. “storeable on thumbdrive”
- huge maintenance burden, especially security, on programmer
- higher memory usage
- big package size
Usually if I see something entirely new (e.g. Marker some years ago) or something using Qt-Libraries (e.g. Zeal) instead of my native Gtk based environment, it is a candidate for Flatpak. Marker is now in native repos of Arch, therefore is use it now from there. While I kept OpenRA as Flatpak because I need usually the on provided by upstream.
I think Flatpak is ideal for new stuff and especially closes-source software. Programmers cannot do the repeated error of supporting some special outdated distributions. It is a miracle to me how anyone can think that packing for a specific distro is their job? It is not. The job is documenting how to package the software and allow redistribution. With Flatpak we allow them to do package themself if desired but just once and for all.
A weak point of Flatpak is that facepalm Canonical is doing it very own show with Snap. How often does Canonical need to fail with Mir, Unity, Upstart and now Snap? The server is closed-source and it is against the community. Even if it would be better it is dead. And no, we don’t need two competing…please just commit fixes to GNOME e.g. type-ahead-find?
And I don’t want to hype Flatpak:
GNOME-Software could use less memory itself, we need an easy approach for payment (and repeated payment?) and it stores many small file on disk. And I wonder which security requirements the Flathub requires?