As a long time JB resident, I'm a believer that the peak hour jam will NEVER be smooth. By the simple logic of imbalance. Also people assume that the volume of commuters is a constant.
The smoother it is, the more people will travel, the more people travel, the more jam it gets. Until there's an equilibrium between both sides, which let's face will likely never happen.
If all the immigration counters at both ends are fully manned, it would go a long way in alleviating the jam, but even that simple thing is not happening.