What I can't understand is why Athletics doesn't come into it. You have enough Athletics, you can jump /up/ 10' (OK, maybe not, even with a running start, that'd be a 50), but you can't turn around and jump back down?
Anyone see a problem with allowing choice of Athletics or Acrobatics (still trained-only)?
Sorta kinda. Athletics is how much/how far, acrobatics is how/in what way? To directly answer your pondering, at the top of the theoretical 10' foot jump, the creature won't have any speed in the downward direction when he lands on the cliff-face, say, and thus won't be harmed by it. If he jumps down the 10' cliff, he'll have 10' worth of gravity to pay for when he reaches the bottom, so how high up he can jump has nothing to do with making the fall any less speedy/dangerous. Based on the example you gave, I see no reason for allowing Athletics or Acrobatics.
However, to take a different route, you can assume that someone with skill at jumping and climbing will have skill in falling, as sometimes you fall while climbing, and you usually fall after jumping. But, on the other other hand, basketball players are injured at least fairly often simply falling from their jumps or from hanging from the goal etc, so maybe athleticism (athletic skill) alone isn't enough?
Say a spiderman type maneuver was required for some reason, like jumping across a pit that had spinning blades that you had to jump through, or to easier to visualize, flaming hoops. You roll athletics to see if you had the strength/power enough to jump far enough to get across the pit. You roll acrobatics to see if you could deftly (dexterously?) fly though the hoop avoiding damage.
As for falling prone, maybe part of the problem is the visualization. Prone (er, despite the term) doesn't necessarily mean the creature in question falls flat on his face. I imagine more of a kneel with at least one hand and one knee on the ground. Acrobatics just means you can roll with it and stand up instantly.
I don't see why you can't use acrobatics untrained to reduce damage though, so Stalker0's solution sounds good to me.