That's like asking, "Which one is better on a Hamburger, Mustard or Mayonaise?"
I, like a lot of others, have only tried the SCT, but only on my previous '08 GT.
I now have a 2009 GT500, with a Procal II, FRPP CAI, and FR500s Performance Exhaust, which is effectively the same as the 2010 Shelby (less the exhaust).
I asked Brenspeed how much more power I could get with the SCT tune on my car, as I am currently peaking @ 513 Max (RW)HP and 485 Max Torq. They told be I could expect another 10-15 RWHP, if I also go with the smaller pulley.
If they would have told me 25-30, it would be one thing, but for me, it's not really worth the extra $379 for SCT (plus pulley, pulley remover, etc...). ...but then again, I don't hold your pocket book.