coming from a guy who's owned 2 Evo's, a MY2000 impreza RS coupe with STi powertrain, a 91 mr2 turbo...basically cars with worthless interiors redeemed by their powertrain...I could not stand the 5.0's interior at all
i passed on a screaming deal about a year ago partly due to this.
as with any car comparison you really need to drive both cars, nothing we say here will weigh as much as your own interpretation of both cars after you've driven them.
what did you like/dislike about the 5.0 you test drove? was it an auto/manual?
putting the massive interior/ride quality/build quality advantages aside, the m3's steering and shifter feel are also much better. despite putting up similar numbers the mustang's handling feel is nowhere near the m3s. YMMV. for an American v8 pony car the Mustang also didn't have as much low end torque as I had hoped for, but this is complete personal preference as the m3 also makes its power up top.
If you are going for the 6mt mustangs be very careful of the Chinese made transmissions, this was the main reason (interior was a close 2nd) I passed on the mustang. To my understanding this issue has been addressed but not resolved.
if you are looking for an auto car then the DCT in the m3 obviously also destroys the auto tranny in the 5.0
stock for stock i don't believe the mustang is faster as you stated, but definitely with just intake and tune the mustang will gain significant performance gains.
Regarding exhaust note don't be too quick to dismiss the m3's...look up some with aftermarket exhaust - it sure surprised me! There's no denying the mustang sounds great though, much better than my Vette's exhaust note even with the Corsa catback IMHO.
between the 2 choices i would most likely still go with a 6mt mustang with 3.73 gear but that's because i get bored of cars fast and the mustang will be cheap to even supercharge and make ridiculous power out of; but i believe once you test drive an m3 the choice will become quite clear for you.