And 'jerk' has to be kept below a certain threshold for humans to find movement comfortable.
It's not strictly a matter of threshold -- people might tolerate a higher jerk if it's for a much shorter duration, for example. In practice it doesn't much matter which metric you minimize; you'll end up with similar results. The simplest option is to minimize the mean absolute jerk, which has the side benefit of utterly confusing any non-physics-literate people listening in. (You want to do what to whom?)
Note that 'mean absolute jerk' can also be described as 'total variation of acceleration over time'. That implies it does not depend on how fast the acceleration changes, only about the difference between minimum and maximum (as long as the acceleration increases/decreases monotonically to/from the maximum). This may or may not be what you want.
It's not strictly a matter of threshold -- people might tolerate a higher jerk if it's for a much shorter duration, for example. In practice it doesn't much matter which metric you minimize; you'll end up with similar results. The simplest option is to minimize the mean absolute jerk, which has the side benefit of utterly confusing any non-physics-literate people listening in. (You want to do what to whom?)