I am finding I miss quite a bit in VATS, but if I want to hit something far away, it's better if I just go into sneak mode, so I am bascially knealing, and snipe the target away with a varmit rifle. I try that in VATS and I miss 100% of the time.
there is an easy way to explain this. real time combat doesn't factor in your actual weapon skill.
you just have to get accommodated to the sway. other than that, there's no influence coming from your stats, skills or level.
basically, fnv mechanically works as a shooter outside of VATS, and as a rpg inside of VATS. that's also the reason why various people already reported of being able to kick major butt with melee or unarmed, while their actual skill was like at around 20.