I owned a 2000 GSXR750, it was a pretty fast bike also (had tons of work done to it, it kept up with a stock 1000). After riding a gixxer and riding a busa, I'd stay with the busa all day. The busa has such an exotic look. I love everything about the busa that my gixxer didnt have- comfort, monster midrange and top end, clock, dual pipes, gas guage, less vibration in the rearsets and clipons, much bigger seat for me and my wife, higher resale value (if you keep it mostly stock), and cheaper insurance (state farm)
Now dont get me wrong, I'm not ragging on the gixxer1000, I've ridden them and they are sick bikes. But in my 6'4", 260 pound chunky opinion, they simply were not practical. I would ride 50 miles on my gixxer, and my hands, back, and legs were KILLING me, I mean stinging burning pain. I can put 150 miles on my busa with no problem at all!
To give you an idea how uncomfortable I was on my gixxer (this was after riding it about 4000 miles) I tried to make the trip from Tampa to Daytona for Bike Week. I made it to lakeland, turned back, put the bike on the trailer and drove it there! I felt like such an panzy ass! LOL
So my conclusion is this, if you are a person who is so obsessed with speed that you will sacrifice all the luxuries of the busa for a fraction of a second faster quarter mile time, for the love of pete get the gixxer!
But for me and my co-pilot (my wife), I got the busa and I'm happier than a pig in sh*t, this bike is just awesome