Shiekh Sb provided excellent review.
Vario is cheap maintenance in parts compare to Vitz/Passo.
Vitz 1999-2004 and 2005-onwards and Passo have better ride quality and grip and suspensions and also smoother engine naturally as they are Japanese and 1.0L.
City has a trunk and petrol tank in between middle of car and its 1238cc twin spark SOHC design with 8 spark plugs and CVT to maximize fuel economy. City has more interior room than all vitz / paso but suspensions are hard and when you go on rough roads the noise of roads will surround in cabin.
It all boils down on your budget and whether you need a trunk.
Vitz 2005 onwards new shape could cost you 7.5 lacs and a much better option with high reliability ABS, Airbags, navigation and better drive than City.
Vario 2003-05 will cost you 6.5 to 7.5 lacs depending on condition and mileage. 2006 to 2008 vario will cost 7.5 to 8 lacs max for a 75,000km driven car.
M/T will cost u 25-50K expensive.
There was also a 1.5L version steermatic but it has worst resale and could be bought for 7-7.5 lacs easily.
If you want to buy Vario look very closely for engine and gearbox as they alone can cost u 100,000 easily if something goes wrong.