On Windows it caused pain from too deeply nested node_modules directories. The underlying file system (NTFS) supports long paths and npm has no issues with them but Windows own tools and many 3rd-party tools fail on paths greater than 255 characters. As a result, packages will now be installed on the top-level node_modules directory. When there is a dependency version conflict then nesting is still used but paths are likely still shorter than before.
The shrinkwrap command got improved a lot. This should also eliminate the package.json/npm-shrinkwrap.json difference issue. I will definitely try again to use shrinkwrap on my Node applications.
The full changelog can be found from here.