I'm not bryce, but to give you a good idea.
A piggy back is a solution to a problem,
A flash is solving a problem. A flash can cover every single parameter of an engine and all of it's safety systems. This makes it possible to tailor it to exactly what your car needs. Granted the flashes are getting really really high tech, however, they will still never solve all problems that a flash can.
as a result, it is easier to get peak power out of at flash as well as the reliability.
Because it is the stock ECU (and this becomes debatable with new technowlogies in piggybacks) the flash adapts to all the normal conditions like weather, altitude and etc. (yes JBx, and procede do this to a certain extent)
The best possible thing you can do for yourself is to get a dyno tune with something like the cobb. The tune is made specifically for your car and it's engine, not everyone's cars. So, they can pull a little more power and do it safely as a result.
One more thing to note is that piggybacks can sometimes be detectable for when they take over the engine parameters. this usually happens at low enough RPM that most people won't notice. Also newer technology makes this less noticeable. But it is something that i feel sometimes on the JB3. But i don't really care, but i do plan to upgrade to a flash at some point in the future (Need to get my new car first
)