I think there are a few concrete things going on:
* There are many more integration points between their products now. Shipping only the Mac or only the Mac and an iPod or even a first gen iPhone that can only get data into system apps via a USB cable is very simple compared to what they're making today. For Apple's best-cast customer, who owns a Mac, an iPhone, an iPad, an Apple TV, an Apple Watch, and who uses iCloud, how many integration points are involved now? Integration points are like the exponent on software complexity. It's where software goes to die.
* They are still essentially a fat client company that's trying to build more cloud-oriented applications. This leads to additional complexity in the product that other companies just don't have to deal with. An obvious example that jumps to mind is iTunes vs. Spotify. If iTunes was just Apple's version of Spotify, how much better would it be?
* Brain drain. Apple's stock made a lot of people a lot of money, and if you work there, you can't participate in the mobile revolution they started. Steve Jobs's passing could also be a natural book end for people in their careers to try something new, or find a job where they're not working 80 hours regularly, or to just take some time off.
I guess the last one isn't really "concrete", and is more just me speculating, but I threw it out there because of a decent amount of anecdotal evidence I've seen. Here are some other things that are also just speculative but interesting to consider:
* Apple is a product company that succeeds or fails on innovation. As capable of an executive as Tim Cook clearly is, he's not a product person. How does this trickle down into the product development process?
* Product development was micromanaged by Steve Jobs basically until he died. That leaves a HUGE vacuum in an organization and executive team he built to amplify his personal strengths and weaknesses. Who is filling that vacuum now? Is it Jony Ive? Does his new role of "Chief Design Officer" mean he's kind of the new Steve Jobs, in charge of product design, retail stores, office space, etc.?
* If Jony Ive has the final say of all software still (not clear to me in this new role), how good is he at software? How interested is he in it personally? He clearly loves the physical design of things. Steve clearly loved software. If Jony is in charge, does he have that love as well? Does he devote the time and attention into the software as he does with the hardware? Or, to take the iTunes example again, is Eddy Cue basically in charge of that product?
* How good are the people there at software design without Steve? There's a great story about Steve Jobs coming into an iDVD design meeting where he ignored what the team came up with and drew a window on a whiteboard with one area to drag files and one button that says "burn".[1] Is that just one story? How important was that to the day-to-day of the products they shipped? Who does that now?
The key point to me is that, according to Steve himself, Apple is a software company.[2] They make hardware so they can make really great software. Software is what's most important, and I hope stories like this are a bit of a wake up call to re-center their focus on what's truly important.
[1] http://dandemeyere.com/blog/5-most-inspiring-steve-jobs-stor...
[2] https://www.youtube.com/watch?v=dEeyaAUCyZs