Fermented soy products are easier to digest. That's the only benefit to fermentation that I'm aware of. Well, that and the bacteria that is used to ferment foods are beneficial in of themselves.
I stay away from overly processed soy, in other words, soy dogs, soy lunch meat, or anything that isn't easily identified as soy. Products that are closer to the "bean" I have no problems with. So, I eat soymilk, tofu, tempeh, miso, and natto (yes, I'm weird, but I love natto.)
I don't think soy itself is bad. I think there are underlying factors that may not be considered in these studies that suggest you stay away from soy. If soy was evil like some people think, then how on earth do you explain the Japanese? The eat plenty of soy and I've never heard of them having a breakout of "man boobs" or any of the other things attributed to soy consumption.
For example, one of the studies that suggested that soy caused Alzheimer's was done in Hawaii. But when they tested Hawaiian tofu , it turns out that Hawaiian tofu was higher in aluminum, then tofu from the "mainland." Hmmm... I don't think you can blame that on soy.
Then there is the GMO thing. I buy organic soy products because I don't think enough studies have been done on the effects of GMOs. That and I really don't trust Monzano to have our best interest in mind.