There's still plenty of ways reference resolution with NuGet can go wrong, even without the GAC. For example, because NuGet allows packages to import .props an

There's still plenty of ways reference resolution with NuGet can go wrong, even without the GAC. For example, because NuGet allows packages to import .props and .targets files you can have packages that add arbitrary references that don't match your target framework or runtime. Now you could say "oh, that's the package's fault, not NuGet's", but often the reason a package includes .props or .targets files is to work around other shortcomings in NuGet.