Whey and Soy manufacturers did a superb job of confusing the public. For few years now the health and fitness community has been drinking up soy.
Then research showed that due to its fast gastric emptying properties most of the protein taken in via whey protein is metabolized and burned up in the liver. The whey manufacturers first responded by increasing the number of grams per serving. Why not? More protein would have to be consumed, thus more protein is sold.
Soy is popular with vegetarians. The Soy manufacturers looked on as whey protein sales sky rocketed, and, in to get their own piece of the pie, they went after the "health" market, primarily women. Many of the studies the soy manufacturers cite are valid, but do not represent the whole picture.
One study looked at two groups of healthy middle aged men that were given isocaloric meals with one group eating soy protein, while the other consumed animal protein. They wanted to find out if there is a decreased propensity of gallstones when animal products are replaced by soy proteins. Very often gallstone accumulation is tied to cholesterol crystallization, so they later examined the participants cholesterol levels.
Cholesterol crystallization was found to be slowed in the soy consuming group. This led to the idea that soy will aid in the prevention of gallstones. Unfortunately, the study failed to address an important point. There was zero control of vegetable intake. Soy is a vegetable and is very high in isoflavones.
There are many benefits associated with the consumption of isoflavones, including a lowering of cholesterol levels. Contrarily, research has shown that the ingestion of meat is associated with an elevated cholesterol levels. This is not to say that people who eat soy will be healthier and have a better cholesterol profile than those who consume meat and vegetables. This just goes to show you that extrapolations drawn from research is often taken out of context and overemphasized.
While a great number of scientific studies can be held up to show the cancer resistive benefits of a diet rich in vegetable foods (soy included), we can not extrapolate from those studies that someone consuming soy instead of milk proteins, egg proteins, and lean animal proteins will exhibit better health, and if an exercise component is included, the conclusions in non-exercising individuals are almost invalidated.
Most of the research promoted about soy is publicized by companies with a financial stake in Soy Protein sales. The Soybean Board is a good example. Very often the elements of a sound study are taken out of context to boost sales of soy.
Metabolically, recent data suggest that you should consume a mixture of casein and whey protein for optimal results. Unless you are a vegetarian, you'll see the best results from consuming a wide variety of foods as part of your nutrition program.