Main reasons for retracting flaps in increments instead of in one go, are safety, workload management and simplicity.
It would be possible to retract T/O flaps in one go, as T/O flap settings are usually quite moderate. This would however require careful pitch control and a lot of trimming and monitoring the airspeed. This would impose unnecessarily high workload on pilot flying the plane, and thus reduce safety.
Autopilot would manage this task quite easily, but then there would be a need for two procedures depending on manual vs. autopilot operation.
Slowing down the process of flap retraction would ease the workload some, but it would not fully solve the problem.
One "hidden" risk in single phase flap retraction is the failure of either wing flap mechanism. This would lead to a much more severe assymmetric lift if not caught quickly. And as the pilot is preoccupied with maintaining correct airpeed, trim etc, it is possible the situation would go unnoticed for a while (planes may have warning systems regarding assymmetric flap configuration, this would mitigate this problem).
So: as the departure phase of flight usually is quite busy, it is by far simplier, and safer to retract the flaps in a couple of separate phases rather than at one go. The crew (autopilot) has time to adapt to the new setting before the next one is selected.
Note: flap retraction during go around emphasizes the aforementiond safety and workload issues.