Supplement manufacturers have done a wonderful job of confusing the fitness wanting public. For the last 5 years the bodybuilding community has gobbled up soy protein.
Then research proved 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 casein 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 went up, and, in to get their own piece of the pie, they went after the "health" market, primarily women. Many of the research studies the soy manufacturers cite are valid, but do not represent the entire 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 linked to cholesterol crystallization, so they later examined the participants cholesterol levels.
The study showed that cholesterol crystallization was slightly retarded in the soy group extrapolating that soy can aid in preventing gallstones. Here's what the study neglected to address. There wasn't any control over fruit and vegetable intake. Soy is a vegetable, and it does happen to fall into the group of veggies that are 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.
Scientific studies indicate that there are cancer fighting benefits of a meal plan rich in vegetables like soy. Most people would not assume that people who ingest soy instead of milk, egg-whites, and lean protein will demonstrate improved health, if a fitness ingredient is included, the study would be 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.
As far as metabolism is concerned it appears that you are best off ingesting supplemental protein from a mix of whey & casein protein. The new protein supplements will hit the market and feature this exact combination of proteins. You are best to include a wide a variety of food as possible in your nutrition program.