In the past, the "Mustang" pony car concept was always about low weight and relatively small cubic inch displacement. Did they got for the 428 SCJ, sure, but that does not embody what a "Mustang" was truly about. The Mustang was a V-8 car....quick...not fast per se with the small screaming 289 and small screaming 302. Hell, even the 351 was a screamer.
To me, the Challenger back then was more of a bigger, brutish car. Higher price tag, more creature comforts, big displacement V-8, etc.
Nowadays, you see the same parallel - with the new 5.0 Mustang is putting out with 415hp - preliminary drag tests range from 13.2-12.8 at about 108mph which is quicker than the Challengers. Past a 1/4 mile? I am sure the brute strength of the Hemi would pull that Challenger past the Mustang. Both cars have aerodynamic issues, so it may not even be able to get past the Mustang at all.
It comes down to weight as far as a 1/4 mile car, the Mustang has and most likely will always hold the weight advantage. Can Mopar compensate with larger displacement? Sure. But then you lose road manners like handling and breaking.
Its all about what you prefer. I am a true fan of both cars. They each do some things very well.