I'm sure there is a difference in engine performance to depending on the materials used .... remember it from my uni days (BSc Automotive Engineeering

)
If you had the same system made from both materials one would give better torque and the other better top end - can't remember what's what though and it's marginally ....
I'd say go for Stainless as you get a lifetime warranty so if it breaks it gets fixed / replaced and it won't rust !
What's the point in spending ?200 on a system that'll only last a year or so !