Having used Lion for more than a month now, I do not understand at all all the bluster about the auto-save behaviour and the disappearance of the ‘Save As’ command. Not having to think about saving just feels natural to me. And duplicate also feels like the more natural way of doing things, since we always used ‘Save As’ as a means to duplicate a document.
Of course, the lack of a default shortcut might trip people up but it is the price to pay for having a stretched-out transition from the old behaviour to the new. Apple probably should have used cmd-D or cmd-shift-D but some people, including John Gruber, feel more comfortable with keeping their old habits, i.e., cmd-shift-S, and/or want consistency among applications as a lot of ‘legacy’ applications still have, and will have for quite some time, a ‘Save As’ command with an associated cmd-shift-S shortcut. Maybe Apple felt no shortcut was better than picking one of the two (S or D), particularly since it is easy to add one yourself.