i have the cortex, they both have the same exact tunes, and can both retrieve error codes, adjust for larger tires etc. the only difference is the cortex comes with a 2 year powertrain warranty, don't ask me how much it covers, i would imagine you would have quite a hard time getting money out of superchips if something went wrong with your truck, however when i bought mine superchips was offering a manufacturers 50 rebate on the cortex making it the same price as the flashpaq so i figured why not.... also the cortex can log data such as 0-60 times, quarter mile etc... the flaspaq may do the same i am not sure.
bottoms line- 1 possibly 2 differences
1)cortex can do data logging (0-60, quartermile times)
2)2 year limited powertrain warranty
my recommendation would be the cortex for the warranty. . . for whatever thats worth, especially if that $50rebate is still going on.