the only real hit will be on the hwy at cruising speed where at a give speed your rpm will be 15-20% higher. In town it'll be easier to get it going and if wanted you can be in a higher gear. I drove both and the 3.31 (or higher) is the way to go. Bad news to make the odo/speedo work properly you need to get a tune or have the dealer reflash for the gear ratio. Ford only supports up to the 3.31 in the V6.
I called a few dealerships around my area and all of them said they couldnt flash my car to upgrade my gears to 3.31. Wonder if anyone else has actually got a dealership to do this for them.