It depends on a few things. 1st, is this going to be JUST your daily driver or a daily driver PLUS a car you'll take to the track? Do you have the money or even DESIRE to start modding the car? Answer that first and foremost.
If it's just a daily driver, either will do. I am leaing towards the V6 myself, but if you're concerned about gas mileage, the Ecoboost is by far the better choice. If it's something you'll start modding, I would then recommend the Ecoboost. As it will most likely respond better to minor modifications.
That said, having owned several modded and high horsepower mustangs, I likely will be buying a V6 next year if GT prices don't drop significantly. I really do not care for stock low horsepower turbo cars (mostly due to them being dogs when not under boost) and have no desire to get back into moddifying my daily driver mustangs.
I admit I can't wait to see some V6 guys putting superchargers on their cars in the coming year or so and seeing what kind of numbers they'll be putting down. I think they will be taking a poop on the Ecoboosts and a lot of stock GTs for a fraction of the price. $22k V6 with a maybe $6k into a supercharge making what, 420+hp? That's some interesting potential.
84Ttop, go pick up a V6 and drop another
Vortech in it. We need some argument data here.