I disagree with some of the comments above....while the downpipe is the most restrictive piece because it is closest to the turbo, it is not the only restriction. The stock resonator and exhaust are extremely restrictive and create tons of backpressure that negatively affect turbo performance, have you seen actual pictures of the insides of them?
While every car is different, generally speaking you want the least restrictive backpressure from your exhaust system as possible on turbocharged vehicles. That being said, it can be counterproductive to go too big in exhaust piping diameter. For our cars, assuming you're pushing less than 400-500 horsepower, a smooth 3" turbo-back exhaust is the most optimal for power. I'm a power guy so I'm not concerned with how loud the exhaust is, only performance. ( I had my wastegates dumping to atmosphere in my eclipse engines which was scary loud, youtube search "dsm o2 dump")
Before I got into my Ecoboost, I owned several turbo Eclipses and Talons and I can tell you that replacing the stock exhaust on all of them (including the mustang) definitely added horsepower. Being able to judge how much horsepower is added on the Ecoboost is more difficult as the airflow monitoring and ECU is much more advanced on the EB, so you don't get the full performance affects of a larger exhaust without a proper tune. Also having a larger and free flowing exhaust maximizes any other upgrades or tunes you may do in the future.
I don't claim to be an Ecoboost expert, as I just got into these cars a few months ago. I realize EB's are unique with regards to modifications, and the stock exhaust is not the most restrictive piece ever made, but everything I've ever read and experienced says that a larger, freer flowing, less restrictive exhaust (compared to factory) on a turbocharged car increases performance. If I can only gain 5-10hp out of it from going big....I will
Turbo Exhaust Theory
Exhaust Systems for Supercharged and Turbocharged Applications
Exhaust Design