I feel the SS lines are a must when looking at better brakes, so that is the first step. Frankly I don't know why a flagship bike like the Busa doesn't have them stock. Add a good set of street pads (like EBC HH's) and you have some pretty good brakes under most conditions.
The stock brakes actually aren't that bad on the Gen II's, their reall issue is lacking feel. I went to the Brembo 19 RCS radial master cylinder. This thing is a real game changer on the brakes. It's forged so the housing is stronger and you can adjust it for power or feel. This thing is no hype job, it's really magic and you will just snicker at the $350 price once you pull those brakes and feel nothing but two fingered, linear sweetness.
You really don't need to do more than that frankly. If you do a lot of track days you might want to look at different rotors to reduce heating of the braking system under extreme usage. But the rotor thing is mostly aesthetics IMHO. The radial MC ($350), pads ($50) and the SS lines ($125) will do the trick. BTW, the rear brakes are really not that important and I actually prefer them a bit mushy so they don't catch. You really don't even need the SS lines on the rear IMHO. Of course if you ride in bad weather conditions you might use the rear brake more than I typically do.
If Suzuki does put out something new in 2011 for the Busa it will be ashame if it doesn't get a radial MC stock.