As for internal consistency - making sure that no game feature is left unused or unusable. This is a bethesda game there are choices within the game that makes other choices obsolete. Take lockpicking/security. totally can be ignored if a magic user. Or do a quick quest and get a key that makes the entire skill near meaningless.
Mods just extend that theme ... but it is inherent in the game as it is.
That's like saying crash bugs are "inherent" to TES games after the Daggerfall release. Yes, they're all over Daggerfall. No, they're not necessary for Daggerfall to be a good game, in fact they're a hindrance. Yes, they should be taken out in the next iteration or with mods.
Security is more powerful than Alteration for opening locks. I need 50 level in Alteration to even open Average locks. Security is just TOO strong, because you can use it to open any level chest easily no matter what the level in security. All that needs to be changed to make security balanced (and therefore useful to have as a major and raise) is to make the speed of the pins increase sharply if you're trying to pick a lock above your level, or something like that. This would be a good chance - it means that a thief, with Security, would acctually be
better at opening locks than someone who isn't. It would be a meaningful choice to take Security instead of a waste. As for that particular quest.. yeah, I think it should increase your Security skill by 25 or so

It IS possible to have reasonable balance in single player games.
Reasonable balance DOES improve the play experience because there are more meaningful choices to make and therefore more ways to play the game.
It's amazing to me that people deny either of the two above points.