Hi Sam,
Try setting the regen at 116% to see if it makes a noticeable difference.
If you are not using a 24V battery, it might be worth setting the battery voltage to match the battery being used, as the replacement controller could be of a more recent design which may not work exactly the same as the original MPIII controller.
The regenerative braking force on my MPIII is very noticeable at very slow speeds, whereas the regen on my MP4 will only engage when I'm going faster than ~6.5 mph and also cuts out completely below 3 mph.
I really prefer the regen on my MPIII because it can be engaged at any speed and will then stay engaged until you release the brakes.
If I freewheel slowly down a long hill with the MP4 and then hold the brake lever in just far enough to activate the regen but without applying the mechanical brakes, the bike will slow to about 3 mph, whereupon the electromagnetic dynamic braking force simply stops altogether, allowing the bike to quickly speed up again until it reaches ~6.5 mph which then allows the braking force to automatically cut in again.
This very annoying sequence of braking and accelerating will continue indefinitely all the way down the hill until the brake lever is either fully released to exceed 6.5 mph or pulled harder to apply enough mechanical braking force to prevent it from reaching 6.5 mph.
Alan