On the face of it, it seems absolutely fine, villain is raising a lot, and its a $2 buy in game, I think you are crushing his range most of the time in this situation and given your stack, seeing him make the call wouldn't be terrible but the only danger is that you're making assumptions from only a relatlively small sample size.

I dont think there is anything wrong with 3bet jamming KQ here against most opponents at this stage with a short stack, in fact, against fish jamming KQ here is almost a value raise because the majority of the time, as I said above you are going to be miles ahead and they are likely to call with hands as weak as J9o sometimes . 

It seems like you already thought about a lot of this which is good and given your stack size i don't think you can justify folding unless the opener is a rock. The fact that he raises early position isn't great but you have seen him being really active and also it's a 6max game so a lot of players at micro stakes might not even be thinking about position at all. 

The villain opens for 3x which is pretty big at 200/400 but if it was me, unless I had seen him raising 2-2.5xish before this hand then I would just assume that villain is pretty clueless rather than he is trying to protect a decent hand etc.

Even if you did run into AA…I think its pretty safe to assume it's the right play.