I just skimmed the PDF, but it looks good to me. He doesn't mention allergies, though. Like dairy, soy is a very common allergen, especially in children. Digestive intolerance to soy is also fairly common (allergies are different than intolerances). Many people live for years feeling yucky until they realize they have a soy allergy or intolerance.

I've heard that people with thyroid conditions or immune disorders, or a family history of either, may want to avoid massive amounts of soy because soy isoflavones can trigger symptoms like fatigue, weight gain, mood swings and depression.

Aside from health, there is some reason for concern about soy from an environmental perspective. One, nearly all soy is GMO; two, massive amount of pesticides and herbicides are used in its cultivation; three, we are over-reliant on it because we grow so much soy to feed livestock, and monoculture is bad for the soil and the local ecosystems. (The answer to this, of course, is for people to stop eating animals.) But I would never advise eating soy/tofu that is not labeled organic, and because soy is in so many processed foods, I would be concerned about the proportion of soy relative to other foods - again not usually an issue for vegans who eat plenty of fruits, veggies and grains.

But my take is most of the arguments against soy come from the meat/dairy industry, and possibly a little bit from breastfeeding advocates warning against soy-based formulas (which I feel is legit). Individuals working in the health industry might use scare tactics to elevate their "guru status" so you come to rely on them for the "truth" (and buy their products, books, etc.).

This is a good piece - http://www.veganhealth.org/articles/soymessina