It seems to me that removing the invulnerability, or near invulnerability as the case may be, from VATS would be counter productive. After all, the thing about VATS is that you have absolutely no control over your character when carrying out the attacks you chose, therefore, the damage resistence was introduced so you would not be in danger of being killed while doing it, which would really make no sense, after all, if you could still move during this time, you would probably survive, therefore, making the player character vulnerable when using VATS would tend to discourage its use, if Obsidian wanted to take out the damage resistence, they'd have to change the way VATS works as well so that you're not an easy target when using it, either make it so you could make your character take cover or move while doing it, or basically turn it into something like bullet time or something, and really, I'm fine with VATS as it is. Besides, if we consider VATS a means of bringing an element of the classic Fallout game's turn-based gameplay into the real time gameplay of Fallout 3, it would have made no sense for enemies to be able to kill you in VATS, after all, in actual turn-based combat, your enemies can't move when it's your turn, they have to wait until it's their turn, of course, going by this logic, if it was really trying to be like turn-based gameplay, it could have been closer if it actually froze enemies in place, but Bethesda obviously decided that slow motion and near invulnerability worked better.
Reducing accuracy in VATS or making action points regenerate slower though would be fine with me, after all, VATS could be a little overpowered in Fallout 3, it's just that taking out the damage resistence would end up instead making it worthless, and if they wanted to do that, they may as well just remove it entirely, since I wouldn't use a feature that would effectively be painting a huge target on my head and standing out in the open, even if it meant I didn't need to aim manually.
You can harm enemies but they can barely harm you.
That's because your enemies can move but you can't, so it was a necessary design choice with the way things were set up, and it's not like having the game automatically target enemies for you is a good enough benefit to be worth being completely defenseless.