The original iPad would scale up iPhone apps, and it would look really ugly - extremely pixelated and a whole lot of no fun.
It didn't take long for most developers to come up with iPad versions of their apps, and now most apps have assets for all screen sizes. With app thinning, you'll only get the assets you actually need.
I don't think upscaling from the retina iPad screen to the size of the Pro will be that bad - certainly not like iPhone to first-gen iPad, nor as bad as non-retina iPhone to retina iPhone.
Now - having said that, I have an iPhone 6+, and it always annoys me when I see an iPhone app that hasn't been updated for the bigger plus screen. The status bar is suddenly bigger, touch targets are annoying large - all that. Bottom line is that you'll notice the difference, but the apps will be useable nonetheless.