You're right that a bunch of what's broken in Debian stems from how naïve APT is — especially the lack of a slots mechanism (they just mangle the package names when there's no way to excuse it).

But the fundamental problem is purely social, not technical. Debian is always ready to introduce a new policy that would require them to screw with all the upstream packages (breaking things up, license wankery, dash, silence in valgrind, etc.)

Depressingly I find myself liking the way packaging is often done with RPMs, especially from vendors — they just make a directory in /opt that bundles any contentious dependencies, and just fucking works. Functionally there's almost no difference between RPM and DEB — it's purely social expectations.