Brother I have kept both the cars brand new.
Both were manual though. City iVTEC 1.3 MT and Corolla 1.3 MT Gli (11th Gen)
On motorway, I found the handling of Corolla very good, mainly because of its weight. It was raining heavily and I didn't feel uncomfortable at 140 kmph. City is very light weight car and it trembles when a big bus passes nearby. I was once going to Faisalabad on M3 and it started raining with wind, the car really sways.
City is more responsive on straight runs and at high RPMs. At low RPM, City has a dead zone. Due to this reason, or the DBW, you don't enjoy driving City on mountains. On the other hand 1.3 Gli MT does not have any issues on mountains. Last month I took my Gli to Kalabagh on A/C with 5 adults. No issues. So on straight run City will lead and on mountains it is Corolla for sure.
Fuel economy City is better if you keep the RPM low but the problem is, City doesn't have much power in low RPMs and when you drive it at high RPMs then you won't achieve that fuel economy.
Interior built quality is same for both the cars, same hard and cheap plastics. Paint quality City is better. Metal wise Corolla is far better. Open the trunk or bonnet of City and Corolla and you will feel the difference. Corolla's metal sheet is strong. City is very light.
For comfort, as you mentioned, Corolla all the way.
Resale of both the cars is equally good now.