I think I'd pick Prince Of Persia, not to diminish Commander Keen a single bit but I always found PoP visuals and game dynamics unmatched for its time. I'm also getting biased for two reasons: I played PoP when I believe I was 7 years old and made a magic impression on me when I first played it and is also is my favourite platformer of all times. But of course PoP lacks of the scrolling at all which is Commander Keen's black magic.
I understand that Jordan Mechner put in a ton of hours rotoscoping the movements. (Example: https://www.youtube.com/watch?v=fCy8WqAgPbY)
On a tangent, Mechner is an incredibly talented (and in my opinion, severely underrated) game designer. "The Last Express" is a masterpiece, and wondrous in a different way.
Yes it is very impressive even today. Those tons of hours on rotoscoping paid off immensely. I haven't played "The Last Express" though I've seen some screenshots and looks a very nice game. Somehow the artwork resembles the style of Alphonse Mucha: https://en.wikipedia.org/wiki/Alphonse_Mucha