This recurring notion that we can either have one thing or another thing - that, for instance, we can either have "stupid" athletics and acrobatics or NO athletics and acrobatics - is poison. It's the sort of misleading propaganda that's fed to us by politicians. Beth should be above that, and people shouldn't fall for it.
Good point, but you'd certainly disapprove of my proposed solution: tie it to Stamina, just like encumbrance. In all honesty having it level by running and jumping makes sense, but then again so would having to train for years to be a master swordsman, or dying from a single stab wound because you can't stop the bleeding. That was the inherent problem with the skills: they were tedious to level, not to mention unintuitive since you had to basically jump everywhere if you wanted to increase your Acrobatics at all.
In all honesty, I think that balance and poison/disease resistance should have been governed by health (doubt it exists at all outside of racial resistance now), magicka resistance by... magicka, and of course running speed and jumping height by stamina. It ties into their new system just fine and eliminates the bad parts of the old system by compromising a bit and keeping it, but simplifying it as well.
EDIT: Also the first thing I'm doing when I get my grubby little mitts on the Construction Kit is diving right into the race definitions and changing their base speeds, if there's architecture in place for such a thing.