You get a huge boost up top (because the 06+ R6 is heavily restricted up there), and a nice boost under 5500RPM (because the 08+ R6 is heavily restricted down there).
You can do way more things with an ECU flash than you can do with say a Power Commander.
Calibrate speedo for sprocket size changes (no need to buy speedo healer!)
Disable AIS pump so smog plates are not required (reduces pop and backfire on deceleration, allows you to run autotune/AFM)
Make fans come on sooner/keep bike cooler
Remove 299km/h top speed limiter (mostly applicable to R1)
Remove throttle restrictions
Disable EXUP code in ECU (so you can remove the big black servo box, no check engine light, no exup eliminator required!)
Disable O2 sensor for less twitchy throttle (so bike isn’t switching between “fuel economy” and “performance” map all the time). Works great for use with autotune/AFM. Keeps the bike way cooler because it doesn't lean it out under light throttle.
Load in custom fuel map depending on your exhaust and air filter setup (can import PCV or Bazzaz fuel maps right into the ECU).
Increase ignition timing.
Enable ECU based quick shifter function should you ever want to install a quickshifter in the future (just need to
buy the $70 sensor, no electronics).
Increase the rev limiter if you so wish (06+ makes good power to +500 over stock, so 16,500 instead of 16,000)
Dual stage rev limiter (set up soft and hard limits so it's not so abrupt when you hit it).
Move fuel injector proportioning to put more load on secondary fuel injectors for better fueling
Reduce engine braking (both street and track/race setups).
Raise the idle (stock idle on the R6 is a little low for best oil pressure and electrical charging).
For a track bike there's other freaky functions like a gear indicator (can't use it on street bike because it disables speedo) and auto downshift throttle blipper/rev match, manual control of EXUP for passing noise tests, etc.
It can work along side a Power Commander (for autotune) or Bazzaz (for autotune/traction control). If not using autotune or traction control you can just remove your PCV/Bazzaz and sell it.