I owned a 2004 zx12r and currently a 2005 Hayabusa. I put about 4500 miles on the 12, and 3000 miles on the busa.
I am 5'7" short. So the busa is worlds better for comfort and control whereas the zx12r sits much higher and the riding position is more aggressive (butt in the air).
The zx12r is just as fast as the busa so thats a wash.
The zx12r handles better in that it feels lighter and you dont even feel like it is under you.
The busa is heavier feeling, but carries its weight when moving, very well. The busa is the more stable machine at high speeds, and frankly ALL speeds. The zx12 has a bit of a shaky front end...and it feels like its going faster than it really is.
The busa feels like its going slower than it really is.
Busa is a better package as far as design and build. The zx12 is thrown together and cheap-ish.
The 12 makes more HP
the Busa makes more torque.
The 12 looks like a sportbike -so if you like that you will like it.
The 12 is definitely very comfortable considering it is a supertrain.
PILLIONS need NOT APPLY on the 12. The busa is better for passengers. You can get a corbin backrest for your passenger on the busa. There is no such item for the 12.
The busa is beauty in the eye of the beholder. I think it is a bit of a fat dumpling looking bike...but I also think the zx12 looks like it was put together in a junkyard, with way too much guts showing all over the place.
Busa for long high speed sweepers. The 12 for sharper more frequent cornering.
If you are tall...the 12. If you are short - the busa. Tall people do not look right on busas, because their long legs on the high pegs -put their knees too high.
The busa has a stock steering damper, and while some have said its useless, I completely disagree. I think the stock steering damper is more than adequate, and it allows me to let go completely of the bars at 130,mph and they track dead straight on.
I couldnt take my hands off the zx12 at 30mph without watching the birth of a tankslapper in the making.
I love my busa, and it is a better bike for me than the zx12r. While the zx12r is impressive, - the comfort factor points me to the busa.
There arent many people who can OUTRIDE the busa anyway. So unless you are some amazing track rider, you will be more than satisfied on the street with the busa.
I used to have a zx11 that I could really get hard on in the corners, - and the busa makes that bike seem like its a school bus.