A 409 works at the frame rate generated by the transmitter, so no real possibility of a change there. Moving to a higher frequency will just cause the motor to whine rather than growl. Careful tweaking of the pots will change the response, but since the output pulses will always start off by being too short to move the motor armature round to the next pole, the motor will always growl, buzz or whine until the pulses are long enough to move it on. When that happens, very likely there will be some inertia built up, and the next pulse will have an easier time kicking the armature round the next bit, so the motor will set off enthusiastically.
At low frequencies, the armature might settle back to its start position at the end of a short pulse, so it has to start all over again with the next pulse. At high frequencies, the armature might not have time to settle back, and so gets a head start with the next pulse.
Bedding the motor in will help, but the motor will always growl a bit when the power setting is not high enough to ensure rotation.
Magnetic cogging is a good thing in most motors - holding the motor by the shaft and rotating the case, counting the resistance pulses until a full rotation, then dividing by 2, is the best way to get the number of poles on a sealed motor. All the pulses should feel the same in a healthy motor.
Although a power transistor might have a rating of many amps according to the datasheet, careful reading usually reveals that that figure requires a very considerable heatsink, just the tab or a small sink requires considerable de-rating.