The main thing I dislike about it assumption that all software should go through the distribution's package manager, instead of application developers distributing their software directly to users.

This assumption has the important consequence that distros don't provide a stable interface (libraries, etc) that applications can depend on. Two years from now your binary may stop working when the distribution updates their libraries.

Most people think the package manager model is an advantage, because it makes installing things that are in the package manager easier, but in reality it comes at a big cost for anything that isn't in the package manager or doesn't want to be in it, including most commercial software.