You're comparison is between 2002-3 City and Vitz 1999(?)-2003(?). I am selecting the 2003 Vitz for comparison:
It all depends on the condition of the used car you're buying, but generally speaking if everything is according to the market average then:
(1) Better fuel average?
Vitz better, because it's a 1000cc car where as City is a 1300cc class car.
(2) Better comfort?
Definitely City. It's more spacious.
(3) Better speed n pick on CNG?
About the same frankly. City might have a slight edge because of being a 1300cc class car.
(4) More durability?
Vitz might have an edge.
(5) And lesser hazel of visiting machenics?
City much better off maintenance hassle wise.
There is also not much difference in price either. If I were you I would go for City. But then I am me and you are you. So it all boils down to what your preferrences are.