ok i've had quite a few experience on this subject. my exhaust story goes:
-stock pipes w/ TRD
(small gain was noticeable since my car was completely stock before)
-2.5' custom pipes from header to TRD
exhaust w/a hi flow cat
(gave me the best gains ever..low end mostly...killed my gas money, and sound was too loud from the TRD
so i had to put a regular resonator in there n that took away the fun. gains were still a lot more than before. the resonator prolly took away 5 hp from the gain i had)
-got hot shot header, and an exhaust leak, muffler shop made custom flangs w/ 2.25 inch piping from header to muffler AND replaced my stock resonator with a magnaflow resonator no more leaks, great TRD
sound. i felt low end go away but top end was much better.
(the reason i chose 2.25' is because the TRD
exhaust pipe is 2.25 inches and that just makes the whole exhaust system even...low end was taken away, but i get it all back in the higher rpm range)
so yea, watever muffler/header you got, if you choose to customize the mid pipes, makin it even is a good idea for better top end gains...
also..sumthin to think about...it's almost like a straw with a bigger top but small bottom...you put it in a cup of water n suck from the big part, but you still get little water flow, so what's the point in makin it bigger. hehe
o n i forgot to end this story with