There are a few reasons why many choose the Cobra over the Saleen.
Performance....Saleens, Supercharged and Standard are 4.6 2V SOHC engines. Yes, the Supercharged ones can run Circles around a Cobra, but compare the price of a S281 and a Cobra.
Looks...Many consider the Saleen "Too Wild Looking". I dont but then again I like Wild Looking stuff, as long as its done tastefully.
The Standard 281 Saleen doesnt offer much more in performance over the stock GT. I believe the only thing diffrent is a Saleen Cat back exhaust and the computer. It comes to 10-15 HorsePower more than a stock GT.
Although they do have a improved suspension.
Lets see....If I were to go out and buy a 2001 Cobra...It would have to be PERFORMANCE RED. I love that color. Red is like my trademark. I think Perf. Red is the perfect shade red. Bright, Vibrant, not Dark or muted, shows the lines of the car real well. Not to bad about showing dirt. I JUST LOVE RED...RED.RED.

If anyone noticed, all of my cars are RED. They will continue to be so.
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64 1/2 "D" code Red Mustang Coupe. 289, C4, Mallory duel point. Ported & Polished 65 heads shaved .01 with 351 valves, 11:1 comp, 1.7:1 rockers, blue wolverine lumpy cam, modified 4100 Hipo 4 barrel. GT Apperance pkg. And to many others to list
2000 Perf Red Mustang GT. 5spd. BBK Underdrive pulleys, Flotech off-road H pipe. Hurst T-Handle, 40 series Flowmasters, Steeda Tri-Ax. Ordered 4:10's.
64 1/2 red 6cyl coupe. Future resto.