Levitation gave the world an extra dimension in Morrowind. Especially with the prison above Vivec en the houses on the east part of the Island(forgot the name). The player had extra choices that made the game world rich and gave a lot of ways to handle your problems. It was taken out because people could abuse it and we don't want that! It is so narrow minded. It is a singleplayer game If it really ruins someone's fun that much it is their fault and their fault alone that it happened. Same for enchanting armour. I never even made on piece of armour with deflect magic on it. The game became to easy for you? Congrats you did everything to make it so. This is not a fault of the game or even a balance issue it is the player's choice and that is what can make a game exceptional instead of great.
Again I feel acrobatics and athletics where taken out because they could be "abused". You could get to places where no one could go. I had great fun alone in Oblivion to jump to get on top of all kind of places. But if you can get to places the devs didn't think of you might have an experience that wasn't intended by the devs. Of course this is an outrage and must be stopped. The game says its about freedom, but more and more choices get cut from the game. Can we only do what the devs intended? Will I again feel that I'm constantly reminded that some stuff just isn't possible. Will this game get more linear with every iteration? Will we get a game like mass effect where you cant even jump? With this I see them taking frenzy and charm out as well. I'm worried. Are you?
You raise some valid concerns, here, although the issues with Levitation are not the same issues with acrobatics and athletics.
My understanding is that with levitation the devs were not necessarily worried that it would abused, but that incorporating levitation meant they would be significantly more restricted when developing quests and instead of making every single quest work with levitation, they found it easier to exclude levitation.
In the case of Athletics, while it might be considered an exploit to allow the PC to get to a point where he can run around like Speedy Gonzalez, since you can avoid all enemies in Oblivion this way, I think it was more a matter of it being a bit silly to level up this skill by walking quickly everywhere, since everyone is going to be doing that all the time anyways except when they use fast travel. Also it makes the horseback riding feature a bit silly if the PC can run faster than a horse.
In the case of Acrobatics, it's possible the devs were concerned about some limitations for quests taking into account jump height, but I think primarily they wanted to eliminate requiring people to hop about like a bunny rabbit everywhere to level up this skill. And can you honestly come up with 12-20 good perks for the Acrobatics skill?