Perhaps provide a list of elements to be shuffled and elements not to be?
Perhaps provide an XPath of elements to be shuffled and elements not to be?
Preserve URI significant characters: /, #, @, ., .., etc.
Save the names table to enable stylesheets and DTDs to be changed with matching names
Perhaps a simple GUI or an improved API
Preserve more non-infoset details: encoding, empty-element tags, references, etc.
Preserve non-well-formed details