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.
The larger point-of-view I'm coming from is the fact that more and more of our foods (and food options) are becoming processed in irresponsible ways contributing to a more widespread malnutrition issue not far in the future. The population is overworked and sleep habits are becoming increasingly worse, both contribute to a reduction in neuroplasticity, for example; ultimately having a significant impact to the populations health.
All things considered it's very possible our medical science innovation falls behind the rate of increase of many diseases. This, in the future, may be directly attributed to irresponsible food industry practices happening right now. Throw that on-top of a huge unemployment wave that may happen in the future from automation, and you have significant increases in socioeconomic costs to any given country.
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.