I've got both a '99 Cobra (Electric Green Convertible w/ Black Top and charcoal interior...luv that Green) and an '03 Cobra. Like most have already said on this thread, the '99 seems anemic compared to the '03. And yes, I do like the seats better, better tranny, ...
With that said, I enjoy the '99 more when open tracking; the car is much easier for me to handle...much better balanced. (Maybe my driving skills are sub-par compared to some.) My performance mods are minimal (Demolet CAI, Bassani x-pipe w/cats, and Bassani catback). My rwhp is ~ 300, and ~ 300 rwtq. In normal driving (not babing it too much), I average 22 mpg combined city/highway, and 32 pure highway. Not too shabby with today's gas prices. Plus, I'm getting almost twice the life from the rear tires on the '99 (I apparantly enjoy the '03s acceleration).
My thoughts: I do like the '03 (and '04); aurguable the best bang for the buck deal going. However for what it is, I would not take anything away from the '99(, though I'm not too fond of the T45 tranny). I don't think you can make a bad decision.
i went from a almost full bolt on, to a 100% stock 03 cobra.
the 99 cobra had 4.10's, dynomax catback, magnaflow catted X, steeda tri-ax, and march UD pullies, it was lowered, mach 1 shaker setup, 01 rear bumper, 01 wing, 01 seats, 03 chrome wheels, and the MM suspension package, including eibach prokit.
then i bought the 03 cobra, and it stayed stock for about 1.75 hours or so, just long enoguh for me to drive back, and put my borla stingers, magnaflow catted X, , and JLT CAI on.
honestly, with the exception of the insane power the 03 has, i honestly felt the 99 was a little bit more fun to drive, i could actually drive the car in the strait line to its full potential, and i jsut dont feel i can do that with the 03.
however, the 03 feels more solid, is quieter inside, and is SOOOOOO much more powerful than the 99 was... especially now, lol.