The main difference is the layout, lets take a look at both of them.
Pure:

Pure Pro, sorry can't find a better one for this one:

We have the obvious ANSI vs ISO layout, but lets focus on the other differences.
Smaller spacebar, 1unit shifts and backspace. right control is in a really weird place!
As for the fn layer, they switched some things around and added a Pn layer. This programmable layer allows you to completely program a layer of the keyboard to your own likings.
I've heard that there are some Pure pro's in ANSI layout somewhere... Not sure where though, heard that Massdrop had them for a while.
Here is a video demonstrating the programmable layer: