After much review and reading we have concluded that the real factor to the aluminum vs stainless debate comes down to $$$$$. Aluminum is cheaper then stainless.
The fear factor is still there for many mainly due to lack of knowledge. I still remember my parents telling me not to use aluminum to cook with. But after more reading and study aluminum isn't going to hurt you unless you are brewing acid, then you have other issues. In fact many homebewers are using Keggles, kegs converted into brew kettles, to boil their wort. Most kegs are made of aluminum, due to the money factor.
This is a great article from Beersmith.org.