My thoughts on package management, and overall system complexity:
Millions of developers are writing code, then many other developers are writing more code which relies on top of already written code, each passing day the complexity of the system increases, but our ability to manage it or even comprehend in its entirety decrease drastically.
You can try to use some chroot magic, essentially making some kind of software API to your system, while you yourself sit in a 'clean' and tidy environment, but what does it solves really? The junk is still on your hard drive, it doesn't matter how you run it directly or not.
Another option is to do it your own way, only clean code, only most sane projects, but then good luck with compatibility, or even finishing such monumental project on your own, it will just make you an elite autist while the rest of GNU/Linux will carry on without you.
Third option is to just accept your destiny, there are no ideals in this world. I personally think that sooner or later the whole software stack will 'explode' into our faces, people will die or lose money left and right because of terrible code, or some bug from 2026 in a 9-level deep library/framework system build on top of ChromiumOS. And it will be perceived as absolutely normal situation, or people will outrage, and ask government to step it, I would love to see how the government will regulate and review 500million of LOC. At least programmers are not going to be unemployed for the very, very long time.