Fallout 3 and New Vegas certainly had some issues with aiming, and it wasn't always related to character skills but rather the mechanics themselves. I play primarily in 3rd person and there were certain distances at which you ran into the problem where your shots weren't going where your reticule was aiming.) Or there have been times when I'm trying to shoot at an explosive object but the auto-aim pulls the shot toward the guy standing behind the barrel instead. Those aren't cases where I'm experiencing wobble due to my character's low skill, which I'm actually in favor of - but rather the fundamental mechanics are giving out counter-intuitive results.
It's also one of those things where you may not always notice it happening, but then once you do it's kind of hard to ignore. For example, the first time I played through Fallout 3, I didn't notice any disparity between my aim and where the shots were landing while in 3rd person view. But then when I went back and played through again it started to creep up on me. Since I was more familiar with the controls and how things played I had more "headspace" to pay attention to the finer details of the mechanics, I suppose. Or I'd start noticing opportunities for exploding barrels and the like more often, start taking bigger chances. After that, it was just hard not to notice every time it happened.
My last play of Fallout 3 I was constantly going from 1st to 3rd-person, not due to personal preference, but just so I could get my shots to line up right in certain situations.
They've said that they put a lot of focus on tightening up the shooting mechanics for Fallout 4, and I'm rather optimistically taking that to mean specifically that these issues have been looked at.
In general, I'm in favor of a bit of auto-aim. This is an RPG, I like character stats to play a role, and that's one manner in which those stats can have an impact. But they ought to, as much as possible, give you intuitive results.