Jon,
People runs secondaries because it is the easy thing to do. You buy the plenum and the piggyback computer and you can get your extra fuel. Stock throttle bodies don't usually accept the type of injector that is required for the power. Stock Hayabusa injectors are good to about 300Hp when you run lots of fuel pressure and increase teh duty cycle. The next step up is Honda CBR1100XX injectors and those are good to a little higher maybe 330Hp not entirely sure as not a lot of people run em. The next step up is Honda S2000 injectors. Those are big, can go to 400Hp maybe. You run em at 28psi at idle because they are so big and you can only take so much fuel out of the stock computer using a power commander. So low end driveability suffers. Not a big deal in this arena but a killer on the street. All those injectors fit the stock throttle bodies on a Busa. Any more power than that and you are gonna need secondaries or a stand alone.
A stand alone can tune and trim large injectors to run well even down low on the street. A stand alone has a relatively higher cost, unless you go megasquirt, and requires a lot of time and energy to put together, get all the sensors working, tune, troubleshoot etc. etc.
If you use secondaries you get to turn your fuel pressure back to normal, and let the stock injectors do the work at low load, which make the bike run like stock down low. The secondaries are programed to come on under positive boost. The secondary computer can be mapped for varying levels of boost so you can change it without changing your tune. A stage one rising rate fmu system can only vary a couple of psi on boost before you need to really change the tune on it.
So a stand alone is best, but if you don't want to mess with spark control and cam position sensors and all that jazz then a set of secondaries is cheaper and easier. The end power ends up being the same, but stand alones tend to have logging and such.
