It's not a fair thing when you think about it, the new Mustang is the new... how can I put it, entry level one in my own opinion. I've given it a bit of a drive, it's preaty nice around corners. But the Vette by all means is one of the faster 'normal' road cars out there, it can take on nearly anything excluding obvuious supercars and race cars on nearly every kind of track in GT excluding rally (maybe).
The mustang is a fair rounded car, can take corners in good stride and has a nice top end, the brakes work well, it's good. On one level, I only say it's entry level becuause it's not quite as powerfull as I would want it, then again it's a new model, and one should not go too overboard the first time anyway. Plus if PD gets it right, we'll get the new GT500 in GT5, which would obvioulsy turn the tables around quite a bit considering that has 450+bhp from a superhcarged V8 against the 2000 vette with 380bhp. Then again the new Z06 has 505bhp and I reckon will be very quick around any track.
I would rather picture the older Ford Mustang SVT Cobra R, least to IRL, I haven't driven it much in GT4 though, but in the late 2000's, early 2001, the old C5 Z06 and SVT Cobra R were comapired a lot at times (and then the superhcagred Cobra with a little more bhp, a lot heavier, but looking more subtle compaired to the Cobra R), I have yet to get used to the Cobra R though, so I can't really give much a coherient discussion far as GT4 is concerned.
Then again far as the Cobra R was concerned, one reviewer from Automobile felt even that was a miss-match against the Z06 Vette, mainly in part to it's weight, and also the fact it's based off the old fox chasis. The new Mustang however to my knowledge is on a newer chasis design, but given it's current power, it can't really be compaired to the more speicalized Z06.
Unlike a standard C5, this new one was based for one off the hardtop which was already the lighest and stiffest of the 3 which included the coupe and convertable. They managed to take out a bit more weight, have a more agressive suspension set, shorter gear ratios, and upped the power, intially around 380-385 to 405 for the final versions. The result was a car that although not having the highest top end, could be a track monster equal to any given Skyline GTR (although my perosnal favorites are the R32 and R34 2000 V-spec 2), Lan Evo, Impreza WRX Sti or as both US and the Japense have been trying to take on, the Europeans with cars such as the wonderufll BMW M3 (standard, CSL

and GTR

...), Ferrari's such as the 360 (the new vette will prob be an aim for the 430... maybe...the F430 is awesome...), some given TVR's, Austin Martins (love the DBR 9), etc.
The current mustang, is a good all around sports car, but it's aim, least the standard version was not so high, perhaps up to the Nissan 350Z which isn't bad at all considering the 350 is a very good car as well, same for the RX-8 (and 7). The new GT500 though, I reckon it could (could) take on such high end models as the Lotus Exige, maybe the Ferraris, a given Skyline GTR, Lan evo, Impreza, Monaro/GTO, and the new C6 (Well it would prob slaughter the new C6 becuase of the bhp differnece alone, corners though, I'd have to honelsty see... I wish they sould sell the car in Britan so they could tear it up around their test track, in my opinion, I think it would be as quick around the track as the BMW M5 if not the new C6 Corvette or Lan evo FQ 320), but not this one in GT.
We could, could go with the option to tune the Mustang to be equal to the Z06's power, but as Ferrari chris put it, it would be a tuned car against a bone stock car.
Usually but really it can only be told by what specefic cars models are in mind, a tuner car usually tends to perform better than a bone stock car, but it all depends on the cars in question, for this case I might say if we have the power equal to the vette, it could turn things around, but then since we have smart people with cars, you don't just necessiarly upgrade only the power, you change everything else to make up with the BHP change, which would make things all the more differnet, but say we only upped the power, it could help, but then again maybe not, someone would have to try it.
It would be me (honelsty), but I can't becuase it's not going to be untill november (maybe) that I can get near a PS2 to do a proper test

. Oh well, maybe someone else.
All in all though, it's not a fair thing to comapre them, a more proper comparrsion would be for example the NSX-R against the Z06, or the M3 CSL, a given GTR 34, an Evo 8, etc.
Anyway, that's my thoughts on it, if I'm off by anything... oh well I guess.
Till later.