The ability to add the keyboard and the pencil illustrates the distinction Apple is trying to make between the Pro and the vanilla 9.7 -- creation vs. consumption.
After all these years, they are still persistently trying to position the iPad as a creation tool. Maybe it will work.
Having said that, I do wonder if one of the unspoken stumbling blocks is that even if an iPad is a great portable computer in many respects, it's only a portable computer. A lot of people "dock" their laptops to get work done. (Or to write comments on Hacker News when they should be getting work done.) I love traveling with my 9.7" iPad Pro and keyboard, but even if future releases of iOS address all the nitpicks I have with it, there are times I want to be sitting at a desk in front of a big monitor. I don't see that coming to iOS any time soon.
* Apple Pencil
* Faster CPU, more memory, more display
* UHD color gamut display (and automatic white balance adjustment)
* Better cameras
I think there are other differences, but those are the big ticket ones.