The reason they call the new 9" iPad "Pro", is because they are charging more for it. Usually they just bump up the specs and add some new features and the price stays the same while the previous generation model gets a price drop.
In this case, Apple has to justify the price increase to the customer with marketing ... And what better way to suggest the average customer is getting more than to tell them they are buying "pro" equipment for a modest price increase, when the exact same model they were considering before the announcement now costs less?
They did the same thing when the MacBook Air launched. They charged more for less, but it was thinner and lighter than the MacBook, so they made that their marketing point by labeling it "Air". Now that the Air line added back a ton of ports, they had to come up with another way to distinguish the Retina MB from them, since they were now selling a MB for a lot more with a lot less. I don't think the iPads raised their price when they switched to the Air moniker, but again that was mostly marketing to set the new design apart from the older one, and presumably drive sales over the cheaper iPad 4 which most people would have been fine with.
The problem is, once they get past that first marketing hurdle and discontinue the product they previously sought to distinguish themselves from, they end up with a name that doesn't really always make sense and causes even more confusion.