The 9.7" has different case and cover colour options, I'd like that in the 12.9" Pro. I have a space grey 12.9" with grey case, grey cover & grey keyboard. I'd be tempted to get a rose gold 12.9" (if released in rose gold in 2nd gen) with pink case & keyboard....but really because I would like a 256GB and mine is 128GB since I purchased at release and didn't want to 'upgrade' to the same generation with more memory.
The grey is nice & practical, but colours just add fun & a bit of personalisation.