I know the biggest debate with a supercharged '07 Shelby GT versus a factory GT 500 was weight..
A small block car (Shelby GT) with similar horsepower (once supercharged), to the GT 500.. (big block car).
Now.. that doesn't seem to be the point.
http://media.ford.com/images/10031/2011_GT500_Specs.pdf
A 2011 GT 500 coupe comes in at 3820 lbs.. I guess because it now has an aluminum block and heads.
Versus:
http://media.ford.com/images/10031/2011_Mustang_GT_Specs.pdf
3600+/- lbs for a 5.0 coupe (plus the supercharger)..
I guess the biggest argument with the Shelby GT versus the much heavier GT 500 was that the small block car handled better, was better on gas, etc...
Honestly, you cannot beat the exclusivity of owning a Shelby/SVT Mustang. If you plan on driving it daily, it might be a bit too much to handle (worrying about where to park it, attention from cops, etc.).
Five years from now, the 5.0 will probably just be a run-of-the-mill V8 Mustang. But the GT500 will ALWAYS be a GT500.. even forty years from now.