Personal opinion...based on my own research...avoid soy.
It is a phyto-estrogen, plant source of estrogen (makes you softer)
It was not meant for human consumption. It began as a waste product of soybean oil expression and was used to supplement dog food. AND if they are now taking it out of DOGfood because of health issues, why on Earth would you leave it in people food?

I have to supplement dietary protein and have been told by my physician and several nutritionists to use whey whenever possible.

I am more partial to whey. Your body is better able to absorb whey proteins and soy can disrupt your estrogen system. That being said, you should focus on getting protein from more natural sources and only use protein powder as a supplement. I try to limit my protein powder consumption to one scoop a day.

I'd have to do more research to answer you, but from some of the answers I've seen suggest some people are using sites that are trying to sell a diet plan. I would be a bit suspicious of information of any kind in that situation. I would suggest looking at a site such as http://www.webmd.com

I have done some more research on medical sites, like the Mayo Clinic website, and have learned a lot of neutral information. If anyone is also confused or just curious about which protein powder is right for them, I highly suggest checking out the Mayo Clinic website. Also, just this morning on my local news broadcast (kare11 in Minnesota) I got more fantastic information as well. Every Monday they hold a nutrition and fitness segment called Motivation Monday where they discuss a variety of health topics. Today just happened to be all about the different types of protein powders and it was quite interesting. Here is the link to their website where you can either watch the video or read the article:

http://www.kare11.com/news/motivation/article/969613/188/Motivation-Monday-The-right-protein-powder-for-you

I thought it was very interesting and helpful!

I'll jump in on the Whey Isolate side...
I use it mainly to supplement my nutritional needs. By adding it to my diet, I am able to hit my daily macro-nutritional goals... I avoid soy products altogether.

I tend to follow paleo
Paleo avoids Soy
While reading what works and is good I found these about soy

http://paleodietlifestyle.com/dangers-soy/
http://paleohacks.com/questions/8094/whats-so-bad-about-soy

I have used both and have better control of diabetes with the whey

Neither! Both are extremely processed and acid-forming in the body. Aim for more whole-foods proteins such as hemp seed protein, brown rice protein, flaxseed, legumes, etc.

You may find this useful: http://thrivein30.com/content/lessons/lesson-3myth-busting_the-whole-food-truth-about-protein-fat-and-carbs/