The only differences being, when you close vim, the scratch buffer does not yield a save prompt, and also, if you open a scratch buffer, then close it, and then reopen it again with :Scratch during the same vim session, any leftover contents from before (but during that same vim session, of course) will be restored, which is neat/convenient. :)

edit: misread your comment, thought you were comparing :new and :Scratch (linked above), not emacs' scratch. Not sure about that one, but again, the 'reopen scratch -> find leftover contents' functionality is a neat thing.