I think the issue with his call to Putin was his own team said "don't do it!" and he went and did it anyway. The circumstances were different, somewhat, when Obama called in the past. And, there is no evidence that Obama violated the advice of his own national security team. What is the value of hiring the "best" people if you're not going to listen to them? I think that is the real issue here. And, it's not the first time. He was specifically told in the past not to acknowledge some intelligence we had from Israel to the Russians and he went and did it anyway, and apparently really pissed the Israeli's off.
Is this worse than the other things you listed? I don't know. It's subjective. Reasonable minds can argue it either way, I guess. Some of the things on your list are pretty egregious in their own right. Do they need to be "better" or "worse"? I guess you can argue about the media coverage of each. But, again, I think the coverage here isn't so much about the detail as the idea that he doesn't listen. If you want to invoke your privilege to make a decision that is contrary to your advisors, that is his right. But, it seems like this is more a screw-up than a decision.
I fully understand that the press coverage of this is more driven by the sheer joy of showing, again, that he's not competent for the job he has vs. reporting on the event itself, but that doesn't mean there isn't a story here and it's not legitimate news. Does it deserve this level of coverage and hyperbole? Probably not.