One of the main problems with the factory programming is the "Adaptive Shift Function". This function allows the PCM to remember scenarios and try to "predict" when these scenarios are going to occur by your actions while driving. While trying to out guess the driver is bad enough, it also causes the truck to shift weird, build heat while slipping clutches waiting for the PCM to decide what its going to do, and causes very unneccessary pressure spikes, thus the "flare" everyone feels.
I shut that off completely. Better to let the PCM base the shifts and such on what the truck/driver is ACTUALLY doing than to try to second guess it.