I've noticed the same thing on the older bikes with cables when riding in first gear, so it's not just an electronic throttle problem. It's also caused by the gear ratio, the extra slop in the gear dogs in the lower gears, and the fact that the low gears allow for more rapid acceleration and deceleration for the same amount of throttle input. The best way to reduce the effect is to use a higher gear. If you add more delay to the ETC in the ECM, it will also affect the rate your throttle reacts when you really want it to react quickly. It's a tradeoff at best.
If I'm just putting around the neighborhood I ride in third gear (5 speed trans) at low rpm to eliminate that sudden on/off feeling. It has the added positive affect of keeping the mechanical and exhaust noise levels down, which neighbors tend to appreciate. Before anyone throws out the old "lugging" red herring, it isn't lugging if you putt around in the lower gears just off idle. Just don't grab a handful of throttle when you decide to take off without shifting down first.
Jerry