It only makes sense that, as you run more, you get better at running. I shouldn't be able to cast a magical spell on an enemy, improve my stamina and become a better runner from that. It makes no science.
Same with Acrobatics. I wish that skills like these existed in there own category, like "physical bonuses" or something.
It makes no science?

I agree though, I liked the mechanics of the previous games, even if they were harder to understand.
I'm going to throw out a similar situation that bothered me in another game: Runescape. That game has a pretty nice skill/leveling system, in my opinion.. or at least it did. There's a skill for mining rocks, for example. The more rocks you mine, the more experience you get. But in recent years they've added other ways of getting experience by doing unrelated minigames, such as finding penguins (?) and exchanging them for experience.. This started with a genie lamp back in 2004 that could grant you a wish to get a bit of experience in a chosen skill. That's not so bad. But how does spotting a penguin make me better at mining rocks? That always annoyed me.