For what its worth, I had the same dilemma when I ended up purchasing mine. I knew I would have to sell my motorcycle for a car, so it was either the EVO, STi, Legacy GT, MS3, 350Z, or Mustang GT. I've owned a 2000 GT before, w/ mods here and there, and it really was a great car. I only sold it because I was at a difficult time in my life at that time, but I should've held on to it.
That said, I test drove the Mustang GT before taking delivery of the MS3. In fact, I spotted the MS3 that I wanted to drive while testing the Mustang. Bottom line is the Mustang is just a great car, but it has a lot of compromises. I personally HATE fwd, and the lack of feeling and control it leaves me with at times. However, I do love turbos! I also appreciate more space available, and the "stealth" nature of the MS3, especially in silver.
Handling wise, the GT really doesn't compete in stock trim, though it isn't bad. Its a good car overall, but it just doesn't have the polish of the MS3.
The car I'd most go with right now, at this exact moment, would be the new EVO. That new body style is so damn sexy, its hard not to lust after it. Yeah its more, but its AWD, and my gut feeling is the MS3 should be as well.