Compared to what?! There's no OS that has historically had better (or even close to as good) package management as Linux, either in the form of apt-get/dpkg or yum/RPM. Nix is probably better, on a couple of dimensions, but to suggest it was a mess before...well, I just wonder what you could be comparing to that would be better?
I.e. you download a zip file, you unpack it into a directory, and here is your entire program. Right there, in that directory, not splattered around the filesystem by the package manager.
That's the way it's done on Windows, anyway.
Not sure how things are these days, but i'm talking about the Win 9x to Win 7 days.
And I don't understand what kind of software you used with that pre-filter. You cannot even install drivers then.
But a lot of smaller programs are available in the zip form, or have alternatives that are.
In short, i prefer portable programs - https://en.wikipedia.org/wiki/Portable_application
But, the package manager knows where everything is so I don't have to (and there's consistency across systems...system python/perl/ruby/bash is always in /usr/bin).
If that's why "it's a mess", then I have to argue that it only looks like a mess, until you get to know it a little better. Package management is the single biggest reason I have never been able to seriously use any other desktop OS over the past 20 years, or so (I have a Windows partition for games and audio, and I've had a Hackintosh a couple of times for tinkering with iOS dev, but Linux is where I get work done).
It crushed my dreams of a small Windows partition + a large data/programs partition :(
Engineers shouldn't assume something is done well because nobody is doing any better. Some things suck and there's nothing to blame but other priorities or sheer laziness.
pkgsrc isn't bad at all, but definitely not better than yum or apt. One might prefer pkgsrc, but one couldn't reasonably say yum or apt are a "mess" compared to pkgsrc.