I too have been using native packages for 25 years and I wouldn't say it have been "fine".
I've had to deal with outdated packages, where to have the latest version of a software you had to compile from source.
I had to deal with 3rd party repositories that broke my system.
I had to deal with conflicting versions of a library.
I had to deal with the migration from libc5 to glibc and God that was horrible.
So yes containers might be a little more complex in its implementation, but it means I can install apps from third parties without touching my system and I love that. My OS stays clean, and my apps don't mess with it.