True Tone is great on the 9.7" and ideally it'd already be on the 12.9". I don't find that it's absence on the larger one makes it a notably worse experience though.
Colours do appear slightly better on the 9.7" but the difference is only really noticeable when I've them side by side.
However, where I do notice a difference is in apps that haven't been optimised for the larger iPad. Marvel Unlimited, for example, looks better on the smaller one as it's not yet been optimised for the 12.9". Images look ever so slightly blurrier on the 12.9", but varies dependent on the quality of the source. Nearest comparison I can think of is on a rMBP, at default res it's a little crisper than scaled ie. 2880x1800, that has screen real estate of 1440x900, is crisper than the scaled res of 1680x1050.
Comic Zeal, in contrast, has been optimised for the 12.9" and looks tremendous. I'm rereading high quality scans of Preacher at the moment and I still pinch myself sometimes as the experience really is that good. It doesn't have the tangible quality of having the comic in your hand, but otherwise it's absolutely an equal experience to the real thing for me, something the 9.7" fell slightly short of imo due to the smaller size.
I should add, the minimal drop in quality of Marvel U on the 12.9" is more than made up for by the sheer size advantage of the larger screen. Plus, I'm sure it'll be optimised eventually - surprised it hasn't been already tbh since comics are absolutely tremendous on the 12.9" and Marvel U should be a showpiece app.