Sir go for an A/T, it is best for Karachi regardless of CNG or Petrol.
IDSI was using CVT, that was a whole different story, it uses a continuous gearing or pulley or teeths whatever you call them and definitely have a rubber band effect, much noticeable after driving a PROSMATEC or a stick shift.
The new City A/T has a much improved power train with a 5 speed conventional clutch transmission with a torque converter.
For cities like Karachi A/T is much more reliable as 80% of the 2003-5 Corollas and Civics I have driven have a messed up clutch and shifter.
Regards