Is this a complaint about the Preview app? Because obviously all other programs you might run in OSX make their own decisions about their functionality. Personally, I always use the Menubar search feature via QuickSilver or the default Help>Search shortcut, CMD+?, so I never even noticed those features have been now hidden behind an option key.
The Duplicate/Save As thing is present in any app that's using the system document-based app frameworks and has opted-in to autosave... you'll see it in most of Apple's apps (like TextEdit, Preview, or Pages) and in some third-party apps (off the top of my head, I know Pixelmator does it, and there are others).
iA Writer is another to go down this route. To be honest, I hadn't really noticed since most of my time is spent in Chrome, Sublime Text, Spotify/iTunes, Cyberduck, and Mail. None of these - even the last - have adopted the new api/framework.
Thank you for this, I had no idea. Further, I have no idea how I would have found out about this if not for stumbling across it randomly online, as the menubar is simply not a place where I expect options to be changeable and there's nothing in the menu to suggest option will modify it.