If you have limited budget, don't have time to spent at workshop, small family like 4-5 people, want excellent AC and easy maneuvering, if your area has weird speed breakers then buy Wagon R vxl.
If you have 5-6 people in family, need trunk and like the city shape then go for City.
At home I had zero meter 2012 City which was given by company now it is gone after 65K+ kms, now we have 2014 Automatic City. City is spacious and it is honda thats it, i don't find anything special in it. I usually take out my Wagon R if both are available.
Wagon R has more powerful AC then Honda City, softer suspension, Equally good interior, less engine noise and better Acceleration. Wagon R is offering more in its price. I have Wagon R, done more than 15k kilometers till today and going fine Alhumdulillah. Average is 14 kms/l with 100% ac, 16.5 kms/l without ac within Karachi city traffic.