Stuff to read: Sending XHTML as text/html Considered Harmful (Ian Hickson). The main issue is that lots of authors are using XHTML doctypes without actually knowing what they are doing.
The Nucleus admin area uses XHTML 1.0. When in debug mode, those pages are sent as application/xhtml+xml to browsers that accept it. The only advantage there is that "UAs will immediately catch well-formedness errors". When debug mode is off, the pages are always sent as text/html. I don't think this is a problem. We're expected to know what we're doing.
The default skin (grey) however, has a HTML 4.01 doctype. Main reason is that I think it's a bad idea to expect users to write well-formed and valid XHTML when editing skins/templates. Actually, we probably can't expect them to write valid HTML4 either :)
btw, the default skin doesn't validate because of the short closing tags (/>), which have a different meaning in SGML.

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