In one application I actually chopped the chopper. Reduced the current draw at slow speeds over a lower but continuous duty cycle. I discovered it accidentally because of a bug in my code, but left it in as a "feature". Probably had something to do with a mechanical resonance.
In another stepper motor application, where I was spinning a large disk, I found a compliant coupling improved the acceleration more than several changes to the drive and code. A few years later I saw where a guy inexplicably moved a stepper motor on a robot from direct drive to doing it through a belt. I think he got the same results I did. The stepper can generate a high impact force, but energy is force over distance, and the compliant fitting allows for that short but important travel.