I understand what you are saying and I tend to agree with you. I believe that releasing the 9.7 Pro really hindered development for the 12.9. There are a couple of things that truly make the 12.9 a much more "Pro" option. First is size. Being able to see more and actually use two apps side by side is great for productivity. Although you can have side by side on the 9.7, the view is very limited on half of a 9.7 inch display. The second advantage is the on screen keyboard. Not only is it larger, it has many other options which allow much faster typing. I believe that the 9.7 should have been called the Air 3. Other than the pencil and keyboard, it offers nothing remotely pro over the Air 2.
Reading the original post from this frame of mind...
Yes, there are material differences to the experience of using the larger or smaller models, just as there are material differences between working on any two dissimilar display sizes. I don't know how this has hindered Apple's product development process, though - we're in the first generation of both the 9.7 and 12.9 models - we don't know what's coming next. If you mean "development of public perception/market share," I'm still not so sure. It depends on what Apple wants the public to perceive about the "Pro" name.
There's the perennial debate here about what "Pro" means, for any of Apple's products. Does it mean, "for professional media creatives," "targeted for the corporate market," or, "top-of-the-line performance?" Absent a clear definition from Apple, it means "Pro" is in the mind of the beholder, and what Apple has wanted us to perceive clearly shifts from one "Pro" line to the next. Personally? I don't care if the thing is called Pro or not. A rose by any other name, and all that. All I care about is the capabilities of the tool.
In any case, I agree, the 9.7-inch iPad Pro could just have easily been marketed as an iPad Air 3, with the primary distinctions between Air 2 and Air 3 being the processor and camera; a typical year-to-year evolutionary change. I guess they didn't want it to be considered a routine change.
Apple apparently does want to distinguish between models that can use Pencil and Smart Keyboard, and those that cannot - would an "Air 3" have come equipped with
those capabilities? We have to wait for future product introductions to see whether Pencil and/or the Smart Keyboard are available for every new iPad.
However, I think the primary reason we have a 9.7" iPad Pro is the corporate market. If you aim to sell tens or hundreds of thousands of units to a single customer, it's more effective to say, "For what you plan to do, you need something from our Pro line, just choose the size that makes sense to you." There's a clear performance distinction between Airs and Pros, which there wouldn't be if an Air 3 had the latest processor. "If you want the large display, get a Pro, if you want the smaller display, get the Air 3. Don't get the Air 2 or Minis, their processors can't cut it."
I enjoy my 12.9" Pro - for some work, I'm definitely happy to have the added size. And I like the full-size dimensions of the Smart Keyboard (not the best-feeling keyboard I've used, but at least I can touch-type effectively). Still, it's a lot to carry around.
Considering what I can accomplish on an iPhone's far smaller display, that whopping big 12.9" display isn't always necessary to me. When I tried out the 9.7" I didn't think Split View or Slide-over were too small. Yet, if the 9.7" model had been available when I got my Pro, I think the Smart Keyboard dimensions would still have tipped the balance toward the 12.9".