I was having the same problem with my City, Vario (2005). It was smooth in general BUT while accelerating from a dead stop, up to lets say 30-40 km/h it jerked PRETTY BAD; i mean serious jolts. First i thought it was a gear fault but after reading through the car's transmission assembly, the gear doesn't have fixed rations on which it shifts, it shifts continuously maintaining the RPM.
Anyways, couple of days back i went to my mechanic, after searching for the solution to this problem for over 3 months on the internet and different forums; the possible problems were
1) Transmission/CVT calibration required
2) Spark Plug/Coil Assembly behaving badly
3) fuel pump/injectors behaving badly
Got the Plugs checked and guess what; the 2 coils at the BACK were melted. the springs in them were dancing around the cup, the plugs were fine.
Drove the car home after replacing the two coils (12-1500) a piece (the rear ones are more expensive than the front ones.)
Happy to report, NO JERKS WHATSOEVER! the car's got it's mojo back! absolutely smooth and without any kind of jerk or judder.