@OP... dun go for advices from people who never owned Vario. It's a great car to have and I have yet to find anyone who has a Vario (which has always been on petrol) and had any problem with the car itself. In fact everyone is absolutely happy with their car's performance.
It's market value is lower than that of manual one just because of one reason only... this car cannot run on CNG. So if you planning to buy Vario and install CNG in it, then don't go for this car. However it is excellent in petrol, the best mileage among all the Sedan cars available here and a great ride.
Someone mentioned gearbox problem ... you get that only when you have had a CNG installed in the car. Even if you remove if later, chances are that the gearbox will still malfunction. So only go for a Vario if it has never been tampered with CNG installation.
Roadside mechanics also do not like the Vario as they do not have much expertise in handling Auto cars, since they have gained experience and trained on Manual cars generally.
Since the car is to be run only on petrol, and people who generally buy this car look for cheaper fuel in the shape of CNG (as they cannot run the car on petrol all the time with current petrol prices so high), that is the main reason the demand is low. Also, people who CAN afford to run their cars on petrol all the time generaly have that much more money to own a Civic or Altis or other expensive automatic cars with better repute than a City. That is the key reason for relatively lower Vario's demand.