I'd probably still want a common repo to get software from, for the same reason we use package managers and repos on Linux. Not to mention that the app store experience is more friendly to the newbies out there. But the 'just download an apk/exe/.app and run it' should still exist as a lowest common denominator. Not to mention that the existence of that possibility will hopefully keep stores in check and not become overtly hostile, since if they do, users can just say 'fuck it' and download their software piecemeal.

In my experience on Linux, I like having a repo for terminal programs, but anything with a GUI I'd rather just install and manage myself.