Alright well i don't know if the Vats system is hard coded but I want to know if you could possibly change how it works. Example:

You select a body part like usual., but instead of firing you can do bonus damage on that limb if you can get a shot on it in real time.

Is this possible?

I am not sure about the question but following the spirit of the post I have a suggestion. If you feel that VATS are some kind of a "cheat" have you tried not using them at all? If that is bit radical for you and you would like some kind of aiding in combat system I'd suggest http://www.newvegasnexus.com/downloads/file.php?id=35823, it still uses AP to slow down time just like VATS but it does no aiming for you and the recent version even takes into the account of the perks that affect VATS.