If MongoDB is a commodity I can gladly stick to the distro version. If I'm developing something of more cutting edge I want and will install the latest version from the ISV repo.
Yes, ISVs have the right o package their software. But as someone who is both a maintainer of a free software project and packages software for a distribution, I can tell you that I definitely do _not_ want to deal with packaging for every distribution (especially if it's some magical "universal" package). I've used enough distributions to recognise that they all have differences that you really can't "just package for every distribution with one setup".
Only by playing musical chairs with the package names to avoid collisions.
And that in turn complicates dependencies.
With functional package management every application and library gets its own namespace. Installing something is a matter of picking individual items from their own namespaces and creating a profile, the union of all outputs of all packages that are to be installed.
This makes it possible for users to install not only different major versions for selected applications but even variants of the same package (e.g. different configuration flags or different compiler).
At the bioinformatics institute we are using this to provide scientific software to cluster users. With Guix, users can create custom variants with very little effort without affecting the system state or other people's software profiles.
There is still a lot that can be done by improving package management systems. Giving up by going the route of appification (like it's done with Snappy or when Docker is abused as a packaging tool) is a bad choice, in my opinion.
The priority for a regular desktop user is a nicely integrated system, and that is something that ISVs cannot deliver because they don't know what to integrate with.
For example, some folks hate the Windows way because it has drawbacks like a different installation look/feel/process for each application, there's no automatic updates (unless the application has it built-in, which most don't), there's no automatic dependencies (so each app installer has to bundle its own versions of things, which also don't auto-update), there's no single place to go to look for a program that does something you need, automated installations are hard, inconsistent, or non-existent, security issues are harder to deal with (some image library issues from many years ago are probably still in the wild, bundled into some old version of some application), ...
Please keep in mind that "just silly" is just perspective and priorities.
So All MS could do was to release a scanner to look for faulty versions, and beg people to pester ISVs about getting updates.