but were probably cut because they needed each of the three macro attributes to have the same number of governed skills. purely for balance, i believe to much balance causes issue with leveling like we saw with enemies in OB. so merging them together would still probably not be an option.
Ah, but if we merged the two skills, brought back Mysticism (as it rightfully should be), and then introduced a new Combat skill, then balance would have been struck more or less. (I'm probably missing one or undercounting but you get the point) This is a time when the games should start expanding the character system, not shrinking it. But then again, considering Beth's continued drive to find a game engine they can stick with (yes they stuck with Gamebryo for a while, but it was vastly changed between the games) is likely to turn that into a very unlikely possibility. Add on top of that stupid pandering to casuals and you got yourself a regression that wasn't always called for to the degree it happened between each game. (Much of the changes Daggerfall->Morrowind were fairly necessary but the Morrowind->Oblivion transition was fairly sad)
Especially in a game where all skills contribute to your overall level, it would be pretty bad to have auto-levelling skills like that.
This is why they should have been expanded (and then merged for simplicity issues. They can be legitimately combined) not just cut. Though the benefits of the Oblivion style perks were not always that obvious (and in acrobatics case near useless) they were a step in the right direction, and if the dodge system was fleshed out better and running dynamics brought to a more realistic level then we could have had two skills (or a Skill) that would prove massively useful for any character.
Plus as far as the whole auto-leveling thing, that's only an issue when you choose one of the skills as a major. And if you do so, then thats your problem. No one's forcing you to do that and before you come up with the whole attribute grind issue, that was only because of Oblivion's terrible level scaling which a lot of times would screw you over even if you meta-gamed.