Price. I was debating over the same thing when I got my 4" I decided the additional $$ just wasn't worth it. Sure the SS will last longer, but how long are you going to own the truck and how long before you want to change up your exhaust, like getting stacks.
Stainless will probably stay prettier (I don't care but you might). As dwanner wrote it will last longer on salted roads. Stainless is more brittle so if it flexes it is more prone to crack (and can be weaker in the curves in the pipe). Not all stainless is the same. Stainless is a misnomer. It is really stain less meaning it is less likely to rust than other steel. It can still pit or rust some. It is harder to cut, drill, and weld. If you weld aluminized steel you are asking for it to rust at the weld.
In the Northeast alum. exhaust does not do too well. Especially where I live down the street from a Hospital they salt the roads like you would not believe. That being said my exhaust is alum...I primed most of it to kinda protect it. I am gonna add some anti-rust spray I got off diesel manor soon too just to protect it some more.
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