Apple has always made controversial decisions of this fashion in its history, many today don't remember because they weren't Apple customers then. I think those who said Steve Jobs wouldn't have let these decisions happen couldn't be further from the truth. But these decisions have usually paid off, there just were less people then to notice/complain.
A lot of the decisions made on the products released last year actually make a lot of sense to me. If anything, Apple should simply stop including the earpods with the iPhone to reduce confusion and waste. Moving away from the headphone jack is not just about wireless and space, but making the DAC part of the speakers/drivers system. The lightning port is destined to disappear eventually too, with induction or wireless charging.
I think a lot of this is the result of Apple being ahead of the curve (and partly driving it), and is consistent with Apple looking ahead and delivering long-term value products. A wise investor would see the stance of the company keeping course for the vision in the face of such bad publicity as a good sign it hasn't lost its edge.