User interfaces are getting better - which means if your UI is good, it is different, thus it won't be intuitive to those who are trained to not expect it.
Often one has to choose to design a UI for the daily use vs. first a time usage. Better to put the clatter in the tooltips than to let them always be in your users way.
Sometimes you need a gentle nudge in the right direction. Now, I personally dislike Metro very, very much. But the "charms" idea seems nice. How you tell the user (that's just started using Win8) how to activate a charm without a tooltip (or something similar)? Tell the user once (or twice), and only after that it becomes intuitive.
Tools to bridge the gap between first use and power use are worth using.
Are you referencing research which says otherwise?
But I agree with the more general principle, if you have to use these to onboard users WITHIN your experience, something has probably gone wrong.
http://blog.kera.io/post/40920774387/web-apps-onboarding-how...