I'm interested in learning the pros and cons of giving WordPress MU its own directory.
The Codex says,
Many people want WordPress to power their site's root (e.g. http://example.com) but they don't want all of the WordPress files cluttering up their root directory. WordPress allows you to install it into a subdirectory, but have your blog exist in the site root.
Other than "clutter control" - what are the pros and cons of placing WPMU files in their own directory?