In fallout 3 I used VATS to try and remind me of the old targeted shot system that fallout 1 and 2 had. In vanilla it was close to godmode but freehand shooting was not very good in fallout 3.

Fast forward to New Vegas and iron sights are in and really fun to use. So I pretty much ignore using VATS other than in melee for the slo-mo kill scenes.

The thing I start to worry about is that my skill with freehand shooting is better than what my character should have, or is it? Is my shooting better than the character should have and thus I am "cheating" the enemies and taking undue advantage of them?

VATS is a more roleplaying form of combat, in my opinion. I prefer that. Aiming freehand brings the game too close to a mere first-person shooter for my taste.