From everything I've read (and some personal experience to boot) for brewing, there's very little difference between stainless and aluminum, until you start attaching fittings to your pot (ball valves, thermometers, sight glasses, etc).
Basically, boil water in the aluminum for some time (I think I did about an hour) prior to ever brewing with it, then do NOT scrape off the oxidation layer that builds up inside - that's pretty critical to keeping the aluminum from leaching "bad stuff" into your beer.
If you're looking to add fittings though, it's best to stick with like metals (ie, attach stainless fittings to stainless pots, etc). There are other combinations that'll work with minimal corrosion (and I'm sure someone will add to this to clarify which) but in general if you can stick with like metals, do so!
