raschemmel:
Speed is set by the PWM duty cycle of the stepper motor.
No it is not!!!
The speed of a stepping motor is defined by the frequency of pulses you give it not the duty cycle.
Stepper motors have no parameter such as Accel or Decel like the AC servo motors do.
It is not the motors that have those characteristics but the motor drivers.
Yes you can have acceleration with a stepping motor and yes you could change these parameters in an interrupt service routine.
The main problem is that the libraries that allow for these parameters are not designed for them to be changed on the fly, so they would be out of scope for the ISR. This can be remedied but you will have to either hack the library or write your own code.