Nope, not at all IMHO. At our shop we put stainless on and aluminized and never noticed a difference. I believe those are one of those exhaust urban legends. If you deal with rust a lot or just don't want to be putting a system on all the time then put stainless on. I put stainless on my blazer because I have no intention of changing it. There are two main grades of stainless, t-409 in a cheaper grade which will turn brownish color and is the main type put on factory systems now. T-304 is the polishable stainless that won't turn brown, but will turn gold due to heat (mainly out of the headers and around the convertor) but we have seen cases of t-304 stainless tips turning gold when pulling heavy loads and so on.
Flowmaster offers t-409 stainless mufflers on certain applications, not every muffler has the option of being stainless. Magnaflow offers every muffler as a t-304 polished, and actually isn't much more expensive. IMHO magnaflow mufflers sound the greatest with a convertor because of the smoothness they have with them, but everyone has different tastes.