I work at a ford dealership and i can tell you several reasons why I personally would rather have a cobra.
The Cobra is designed to production quality and as such has a decent warranty and is easier and less expensive for someone to diagnose. This is because the SVT PCM is designed for the car rather than Roush which has chips that alter the factory programming and as such voids the actual ford warranty (Ford issued a memo that ANY vehicle containing an aftermarket chip voids the ford warranty). A chip is also VERY easily detected because if someone has to hook up a scan tool, the vehicle shows up as an australian/european car (forget why they do it, but i think it's because other countries have less stringent emissions so it's easier to alter the programming). So in other words, you have to have a Roush warranty.
From personal experience with a drivability concern on a Roush F150, it takes FOREVER for Roush to re-imburse the dealership for the money, which makes them much less likely to work on it. Plus only Roush dealers are usually willing to work on the vehicle whereas non-roush dealers would probably make you pay for repairs out of your pocket or they wouldn't work on it at all in the first place.
The Roush has a cheesy body kit that is easy to scrape into things and basically all you get is a GT with ground effects, side exhaust, and a supercharger with related engine management items. The Roush air filter and housing are cheesy at best as well and their "electrostatic welding" of the air box isn't very good (they call it electrostatic welding....i call it cheap glue).
The Cobra also brings the name and good handling in a very daily drivable package as well as good emissions, whereas the Roush rides rough and for the money isn't all that great (in my opinion).
This is what i think...i'm sure there will be differing opinions though
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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