Can you tag Medicine, Repair and Barter, and focusing on those skills, still be able to complete the game?

Sure. We recently had someone play through the game and finish it while only killing one thing very early in the game...a Radroach. I'm not saying I recommend everyone run out and try to play the game as a pacifist, but if you want to give it a try, it has been done.​

Is the Intense Training Perk (permanently raise one SPECIAL) a one time use Perk for one attribute, or one time use PER attribute, meaning you could spend 7 Perks/Levels upping each of your SPECIALs?

You can use it more than once, so yes you could keep upping each of your SPECIALs, but that's going to come at the sacrifice of being able to do quite a bit of other stuff with available Perks, skill boosts, etc.​

Specific body parts cannot be targeted when fighting with melee weapons or in hand to hand combat. What is the reason behind this decision? Does melee/HtH fighting offer something else to compensate?

We tried many ways of doing melee with VATS, and having messed a lot with "missing" in melee, it just felt really bad. So once we changed VATS melee to "always hit", assuming you are in range, the body part selection became a bit unbalancing, so now it's a "whole body attack", but you still do end up hitting a specific body part when you swing, but it's based on what you actually contact with, as opposed to what you aim at. This avoids the "always punch in the head" problem, whereas with guns, we can balance out certain body parts with hit percentages, like the head.​