City is a compact sedan and 1300cc, depending on the model and version, being filer/non-filer, buying brand new vs used, your daily commute, type of commute, general occupancy/carpooling needs, technical know-how, etc.
City, manual gives good average but auto is 10-12kpl whereas vitz auto gives 16-18kpl, city has four tiers of token taxes i.e: pre-2017 and 2017-onwards (4500/9000) and (7500/13500) filer/nonfiler respectively. Vitz has lifetime token no annual taxes.
Do you know how to keep a JDM fully maintained including preventive maintenance? Whereas honda is a turn-key solution and if you follow their timely maintenance schedule you will never have reliability issues.
Do you work/carry with a lot of stuff? Do you travel highways with luggage a lot, City has a larger bootspace than corolla. Whereas Vitz is a hatch and even though rear seats can be folded to extend it its still no match for a dedicated boot.
Do you travel highways or smooth roads , or in stop and go traffic in the middle of the day and must need an auto.
I think both cars are great and you simply cannot go wrong with either one of them. It is like choosing between katrina kaif and pretty zinta, there are no wrong choices just make sure whose nakhra you want to pick.