Problem is emissions, because two things are happening to make the throttle response jerky:
1 -- the Air Fuel Ratio is around 14.7 parts air to 1 part fuel at low throttle positions... as ideal as that may be for the environment, it's not a smooth throttle but a jerky one. Idle is fine at this AFR but otherwise it needs to be 13.2 to 13.6 AFR for smoothness. A narrow band O2 sensor on the latest models keeps it around 14.7 AFR... so there you have two options. One is a narrow band sensor controller to richen up that area, and I'm not sure if that's available for the late models (look for a sensor at the exhaust collector top-side to determine if you have the sensor). The other option regardless is a Flash Tune to both remove the closed loop tuning at the low power settings and properly set AFR.
2 -- whenever you let off the gas at almost any RPM, the bike is tuned to run on very little fuel, which is a super lean condition, and as soon as you crack open the gas, it surges. Again, this is for emissions. This can only be fixed by a Flash Tune also, and can also reduce engine braking a little which helps (even with the slipper clutch)
This seems to be an known issue. It's difficult to smoothly crack open the throttle a little, or to roll off that last little bit smoothly. Disrupts my turns. I'd like to fix that!
I was thinking about the throttle [position] sensor. The service manual has specs on it, but it also states to not remove or adjust it. Has anyone played with that sensor?
Of course, I'll check the throttle cables. What else might cause the problem?
Arizona is describing DFCO. Deceleration fuel cut-off comes on when you cut throttle and the engine is above idle, it'll shut off the fuel injectors until just above idle. This was what was actually the issue in the first year of ninja 300s was that the ECU wasn't turning the injectors on soon enough so the engine would stall. This was originally set at around 1000 RPM but when you'd pull the clutch in at the tail end of a stop where you were higher than idle, the bike would die because by the time the fuel kicked back on, it wasn't enough to keep the engine running.
I believe the issue you're experiencing with the jerky throttle is more due to the cheap ECU and TPS. Other modern, and much more expensive bikes with better ECUs and sensors also have DFCO and adjust fueling at low RPMs but don't jerk when you let off the throttle or crank it back on.
I personally believe the issue is that the TPS isn't 100% calibrated true to the actual throttle and can't be due to the cheaper design of the ECU and sensors. That jerking you feel when you let off the throttle is that just BEFORE you've closed the throttle all the way, the fuel is completely cut and you notice it as sudden engine braking at partial throttle. When done properly, the fuel cutoff happens right when the throttle butterflies close so you wont get any jerking. The problem is that with the throttle partially open, it's still pulling in a good quantity of air, but loses fuel just before fully closed and this sudden loss of power is what you're feeling.
It's the same when you're rolling on the throttle. You roll on the throttle a little bit and the butterflies start opening but the ECU and TPS hasn't quite caught up yet. You now have the engine sucking in quite a bit more air in than it would at idle and then the fuel hits and it's a very sudden burst of power.
TLDR: I believe it's a consequence of a cheap ECU and it's throttle monitoring function which can be masked by enriching the fuel mixture a bit to cover up the flaw.