But then anything can be a skill. Breathing could be a skill. Eating could be a skill. Alcohol digestion should be a skill.
Stupid examples I know, but my point is anything can be a skill in a game like this. It's a case of is that skill actually useful and used by many, With the case of acrobatics and athletics, they weren't.
You are speaking too general while you shouldn't.
Acrobatics and Athletics where useless TO YOU not to everybody.
Not everybody has to adopt your playstyle simply because you like it.
What Bethesda has done in Skyrim by removing things like Atheltics,Acrobatics,the Disposition System and its accompanying spells is to limit gameplay variation and force specific playstyles to some players.
I remember 2 builds of Oblivion characters I used to role-play.
One of them was a charismatic bard.He had a natural charisma and people liked him,and he was very social and wanted to make people like him, so he would be the guy who would meet everyday different people and talk with them,tell them jokes,admire them and do other stuff to make people happy. He was a pacifist character that didn't liked fighting so he mostly completed non-battle quests like those that are completed only by speaking to other people or doing small puzzles.
I spent many many hours with that character travelling to the cities of Cyrodill making people happy,solving their problems the nice pacifist way and acquiring their love and money. I had lot of fun doing it.
Now in Skyrim there is no disposition meter,you don't know if you can alter someone's likeness to you or not,and all the Illusion spells that where used to charm people and make them like you are gone!
A whole unique gameplay style is lost,and along with the many hours someone could spend playing that way.Perhaps that was never YOUR playstyle and you don't care for the loss of an attribute,a skill,a meter,a minigame,and many spells that where making this playstyle able,but that doesn't mean that because you never played that way that others didn't do.
Another of my loved character builds was a super flexible Khajit that decided to become the fastest,most agile character in Cyrodill.He would train his speed to become the fastest along his race.He was an athlet.He also liked to do acrobatics.Jumping to places others couldn't jump and laugh at them from above.The existence of such skills as acrobatics and athletics allowed me to set my own goals or 'quests' in the game and try to complete them,and I had fan doing it.Perhaps you never wanted your character to be an athlet,but not everybody has your tastes.
My point is that by removing various features like some skills,attributes,spells etc,the variety of things you can do in the game is shortened.
Sure Skyrim is still a very nice game,BUT it is more directed and close-ended. Sure it's open world and you can go wherever you want any time you want,but the things you can do in the game and the gameplay variation from which you could choose your playstyle has been shortened.You might have a specific playstyle in your mind that suits your taste and happens to be included in the playstyles that Skyrim allows you to choose from.But that's not the case for everyone.
Generally speaking,the more options you have to engage in a situation is better,no matter a game's genre. One of the things that made Crysis a popular game except from its graphics,was that thanks to its nanosuit it allowed you to choose between a variety of ways to engage.You could turn nanosuit to cloak mode to play stealthy or turn it to strength mode for devastating mellee attacks or to speed mode to run fast so you can run past guards...
Variety in gameplay is a desired feature,and in TES gameplay variety is to come with the variety of many different factors like attributes,skills,guilds,spells etc.
Limiting the variety of these is limiting gameplay styles,or ways to engage situations,thus its limiting somewhat the overall freedom you have since the fewer the things you can choose from,the more forced you are to adopt a specific playstyle.
I for once wish that in the next TES game we will be handed with a larger variety of gameplay styles,a larger variety of options to engage situations,so A) more people will be able to choose their favourite style and play that way,and
the replay value of the game is greater.