Apple has never been afraid to cannibalise sales of its on products when moving into new markets. The iPad Pro continues this trend by competing directly with the only recently launched MacBook. With the addition of the (horrible, horrible) keyboardcover to the iPad Pro the two devices are close enough in price to compete directly.
The MacBook runs OS X and has impressive expandability by virtue of its future-proofed USB Type C port. That means full applications, expandability and true computing power.
The iPad Pro means iOS, a much more limited choice of applications and very limited expandability.
It all hinges on the Pencil. Does your normal workflow require the use of stylus to a degree that you would forego the MacBook's superior form factor to get it?
For enterprise customers who offer Apple products as a user choice it will be interesting to see what the take-up is.
My view is that the iPad Pro loses out in this comparison for the same reason it loses out to the Surface Pro 3: it's a companion device. Like its smaller siblings it can't exist as your only computing device. Making the MacBook a generally better choice.