I doubt that the colleges really put more value in one essay prompt than another. A good writer should be able to respond to any prompt no matter how horrendous, generic, or unique it is. If you wrote really well in one of the essays but were mediocre in the other, you'd have an advantage over someone with two mediocre essays, but you personally would probably be viewed as an inconsistent writer and that would be a bad thing not a good one. They wouldn't, for example, just look at your good one and say, "Oh, well this is good so the other must have been a blip. We'll just assume he's an amazing writer."
I always figured the main purpose of supplemental essays were to get you to write about things that the college was interested in knowing, not because the CommonApp prompt "wasn't good enough".