The one true advantage to using a fuel controller instead of flashing the ECU is that you can change the mapping a lot easier with a fuel controller vs. a R.F......but, if the ECU is flashed properly, based on dyno testing for a particular exhaust, you aren't going to be changing the mapping anyway.....so it's kind of a moot point.
My FZ09 has had a R.F. and the difference between stock and R.F. is like night and day. Fueling was matched to the Arrow full system I'm running (without the D.B. killer installed). I also had the flash take care of the start up mode (it now defaults to "A" mode instead of "STD" on start up), and the fuel cutoff on closed throttle was disabled, which makes the bike's throttle a lot less touchy/jerky, when getting back on the throttle after closing it. The FZ09 come with a 132 MPH top speed limiter also, and that can be disabled, although at the time I had mine done, they had not figured out how to do that, so mine is still top speed limited, which doesn't really matter to me since the FZ is not my track bike Lots and lot of options for the flashing method vs. just a fuel controller, but you still have to weigh in the cost of each and determine which one of the methods will work best for you.