To be fair, it was always kinda ridiculous that there was a jumping skill. I mean, you might as well have a breathing skill, or a carrying skill. Its not like this was a Deus Ex situation, where the level designers built in challenges for your acrobatics skill. All that changed (or could change) between someone with 0 points in Acrobatics and a master was that the master could be a jerk and repeatedly jump over the heads of civilians while messing around in towns.
While I agree with you, acrobatics was never really my thing..... It did allow for more RP options. An acrobatic Bosmer who can jump and slash at you at the same time. (jumping and swinging was a "perk" of having high acrobatics in OB)
Athletics makes more sense to me though, over time your character should know their body better, and get winded less easily if constantly moving/sprinting/swimming. Neither of these seemed worthy of being official skills in Skyrim, unless, as you said, it was designed into the game to be more useful.