1. Yes, bad things happen when you don't have enough of all the amino acids. That's malnutrition. That would only matter if you ate soy and only soy.

2. Not all pesticides, just some, but yes that's true. But that's not specific to soy, it's specific to all crops. And crops are washed, you generally don't get significant doses of pesticides in your food.

3. The whole microflora mental health connection science is in it's infancy. The entire thing reads like 6 degrees of Kevin Bacon: some microfloura produce neurotransmitters, which can affect the gut, which can cause an immune response, which can cause inflammation, which is associated with certain psychiatric conditions. I'm not saying there's nothing there, but we're years away from having a more complete understanding. Of course, I have no idea what this one has to do with soy.