I went from a 2010 GT500 to this 2011 E92 M3.
From a pure performance standpoint its hard to beat the GT500, especially if you want more power, but its not a well engineered $50K+ car. Its a 25K mustang with a lot of tacked on parts. Its a bit on a gaudy side, even without stripes its a magnet for every wannabee street racer around, the LED interior lighting is ricy, the lit up SVT door sills are kiddy stuff as well. Quite a few of them have a 1-2 shift problem, they grind or just wont go in 2nd at wot throttle near redline. Mine had it, ford has no clue how to fix it.
Besides the 1-2 shift problem, mine had horrible panel fit, was a rattle machine, rear end carrier bearinggs went out, gas gauge died, interior LEDs stuck on wrong colors many times, stereo was an absolute joke soundwise (shaker 500 w/nav/sync). I sold it off with 2000 miles on it, one of the worse cars quality-wise I have owned in years. Dealer was terrible, wouldnt give me a loaner after they screwed up the rear end and the car sat for two weeks. I got decent money for it and one of the happiest days in my recent life was when I seen that car go.
OTOH, I have a 2011 GT with no options except the Brembo brakes, paid a llittle more than 28K for it. I am going to make a race car out of it but I've been driving it around for a week or so and IMO for what you pay for its a pretty good bargain. The GT500 is probably worth the extra 25K or so, but IMO a regular GT with a supercharged 5.4 and suspension out of the GT500 without the goofy Shelby graphics and body stuff for 15K less would be a hot car.
As far as the mustang vs M3 comparison, believe it or not the M3 has more rear seat room, annoying thing with the mustang is the seats dont fold back to where they were after you let someone in the back. As far as I know you cant get heated seats in the GT500, cant get a power passenger seat either in the GT500 and if you wife is short she wont be able to see much since the pass seat is on the floor and doesnt adjust up.
Really the main difference is the overall fit and finish of the Ford compared to the BMW. On the BMW every wire is in place, it looks like someone actually cared when they screwed it together above and below. None of that stuff really means much to many people though, the GT500 will put a smile on your face for sure, if you can get it in 2nd and the wheel hop doesnt get you. There wouldnt be much of a race between a GT500 and M3 if you could get the mustang to hook up, in great weather a 2010 GT500 has gone mid/high 11s in the 1/4 with slicks, 2011 should be faster. The weights are similar, and a long stroke 5.4L V8 with a positive displacement blower is a torque monster for sure.
Do I miss the GT500? Nope.
Do I like the 2011 GT? Yup, but its a 30K US built car and shows it.
Which car to I prefer to drive every day through the mountains? The M3 for sure, the only way I can describe the handling is 'slot car.' I usually go through the Dragon (US129) twice a week so I gave both a workout. The GT500 will try to kill you, often
Granted the 2011 SVT has better suspension but I bet its just as scary when you get into the rougher pavement.
Sorry for the long post, unfortunately I got a 'bad' GT500 and a bad dealer to go along with it. Lot of guys love them, have to figure you are getting a built engine, decent brakes, double disc clutch, good sized fuel system etc over the GT. You would easily spend more than that on a regular GT to get the same performance, handling and reliability - and its all under warranty. I'm using the GT for a drag car so I can care less about handling and braking, just looking for the least amount of weight..
Good luck, not a bad situation to be in
Oh, and dont forget to check out the 2012 Boss 302 if you are a track guy.