I'd say sometimes it's better , sometimes not . I've had a few GSXR's over the years an' Ninja's an' yadda yadda....
Sometimes you lose a little "driv-ability" with an' aftermarket system . Some of them take away a little bottom end (low RPM's) in exchange for better mid-range an' of course top end. Which can make it a little harder to get off the line smoothly , especially when carryin' yer favourite lady friend. You end up having to rev it higher , an' slip the clutch a little,in order to leave the line without depositing yer pillion on the ground .
I'd be interested to see if its been properly tuned for the new system . You wanna talk to who ever installed it,or a trusted mechanic . Have a look around yerself for a Yosh box , a Power Commander , etc . They usually get hidden under the hump/pillion , the pilots seat(not usually on a Busa thou) , or the cavity under the fuel tank .
If its not properly tuned , yer lookin' at 2-5 hundred in parts(Yosh,PC,etc) , 2-4 hundred in labour(dyno,mapping,etc) , depending on where you live.
Lets us know what the system is an' we can help you from there .
Hav a good 1.....welcome to Busa Heaven....RSD.