Yeah, homebrew isn't the greatest by any means, but it seems to have more stuff and more people use it than fink or macports anymore, so usually there's a workaround somewhere.
The MacOS "app bundle" is a really cute solution to the installation/library problem, and I wish something like it had caught on in the Linux world. It seems AppImage is heading this way.
App bundles are neat, but when given the option of "an app directory on top of a traditional Unix filesystem layout" or "everything is packages", I'll tend to choose the latter. It might just be an impasse situation; I think the ideas of package management are developed about as far as they can go, even newcomers like Flatpak can't really bring anything new to the table. The only package manager that's impressed me in recent years is Nix. I think if most developers decided to throw their weight behind Nix packages, we could live in the "it just works" utopia that Linux and Mac developers alike have been dreaming of for years.
The bane of package managers is when you have to go beyond what they supply for whatever reason - horrible memories of trying to upgrade php on old versions of CentOS still haunt me.
The MacOS "app bundle" is a really cute solution to the installation/library problem, and I wish something like it had caught on in the Linux world. It seems AppImage is heading this way.