I think the problem with iPads (their general flagging sales, not just the iPad Pro, but it'll greatly impact it as well) is that by Apple's logic, it should have an OS all its own. iOS is really meant for lightweight, fast navigation. I like it on iPhone so much more than Android because I can navigate so much faster, everything is clearly organized and labeled, and in my opinion, a phone does not need a filing system. With a device the size of a phone, the simpler it is the better.
In the same fashion, Mac OS is perfect for Macs because while it's still mostly straightforward, it has more functionality since you have a bigger, more powerful, more expensive device to work with. Filing system, Internet app downloads, trackpad/mouse for more nimble navigation, all that stuff.
The iPad, per Apple's mantra, is a device somewhere in the middle that should be able to replace a lot of people's laptops. Steve Jobs's big claim was that eventually computers will be like trucks: everyone used to have a truck, but now just some people have a truck. Trucks still sell, but they don't sell as much as a sleek, lighter sedan (an iPad).
But the problem we're seeing is that the iPad needs to grow into its own. Instead of running a blown up phone OS, it really should run its own OS that's more powerful than iOS and less powerful than Mac OS. Then they could really go to town with Apple Pencil and keyboard functionality exclusive to iPad. That would make it a much bigger draw to me and, I suspect, lots of other people. Have it support old iOS apps, sure, but a design that's a bit more compelling than a grid of apps on a 13" screen would make a world of difference in getting people interested.
I'll also throw my two cents in and say that it's a bit rich for Cook to call the Surface Book diluted when the iPad Pro is launching with a keyboard accessory (for when it stands upright) and a stylus (for when it lies flat). C'mon Apple, if you're going to claim you have a "clear vision" then pick the one you think is best for the iPad and stick to it (I'll give you a hint: it's lying flat. Laptops have screens facing you; tablets should differ if they're going to be their own category, though I'd love to see some technology that makes typing on a glass screen... Less like typing on a glass screen).
In general I feel like Apple is doing great on hardware post-Jobs, but they don't quite have things running smoothly with their software. Not that I'm an engineer, I'm aware that software is pretty much impossible to make perfect, but late 2000's Apple software, from what I can tell, was about as close to flawless as you can get.
Maybe an OS for each device, and two year revamp cycles instead of 1? I mean keep releasing patches/updates, but maybe if there didn't need to be a new OS X and iOS every single year the software guys could make things run smoother.