I suspect it begins with Jony Ive quitting (his official title has become more and more vague over the years, and he's spoken openly about being near the end of his time), and Tim Cook (keeping the company very much afloat, but desecrating brand image) being 'pushed' out shortly after.
There is nothing really wrong with Tim Cook; I think the problem is much more one of how Apple has been structured over the last couple of decades, and the blame for that can be laid at Steve Jobs' feet.
Any corporation, especially any large corporation, needs to have a raison detre -- a simple goal, that everyone in the company can understand and get behind, and that the leadership can use to plan their future actions, or make course corrections when necessary. For an automobile corporation, that might be "make the highest quality cars in the world", or perhaps instead "make the most affordable cars in the world". For a computer company, you might expect "offer the latest bleeding-edge technology", or "provide a wide range of products so that every customer can get exactly what they need".
In Apple's case, the fundamental goal of the company has been "create the products that Steve Jobs wants". Without Jobs at the top, the fundamental goal has become more fuzzy. Tim Cook has invested in what has been most profitable in the past (and so Apple has continued to make great profits), and in the various research efforts (and so Apple research has continued to proliferate wildly); but the soul of the company was not its historic product line, or a wide group of talented technicians. The soul of the company was Jobs, and without him, the company has simply lost track of where it was going.
This company still needs a Cook, and even an Ive. These people are extremely talented. But those people need to be focussed in a direction that will keep the company alive a decade from now, rather than in a direction that will keep the company alive next fiscal quarter. I think that's all that's really missing here...