Good question, I checked both out, and the GT too. I could have gotten either of the 3 and the things that sold me on the Mach1 are:
1. The old school theme of the Mach's design.
2. I wanted the handling of the Cobra but I love to burn rubber and the solid axle rear in the Mach is a better platform to do that with. The money saved over the Cobra could be spent to improve handling and performance to my liking.
3. The Mach1 identifies itself, IMO, better than the GT or the Cobra.
4. The extra 10 grand I would have had to spend for the power of the Cobra vs the Mach could be spent on the Mach in ways that I wanted, which would give me a more personal Mustang and IMO a better package than Ford provides.
5. I like the 4 valve engine and the aluminum block in the Mach1 which attributes to a better balanced vehicle. Although it is not as strong as the cast iron block I beleive the HP can be had to equal the Cobra without jeopardizing the strength of the Mach1's block.
6. I researched and found a larger base of aftermarket parts that I would be interested in for the Mach1 over the Cobra.
I'm sure I could think of a lot more but right off that's the main reasons for me. I like the Cobra for sure and have a great respect for it but being the type person that likes to modify things, my Mach fit s me just fine.