If I recall correctly, the generation of Vios being asked around year 2015, the more efficient one was actually the 1.5, even for city driving.

The Vios gen here bulked up but retained the 1.3 engine.

When the first gen Vios came here, the 1.3 was more than ample and it definitely was a fuel sipper. The main advantage of the 1.5 was the available power. Uncle owned a 1.5L first gen AT and that was a blast to drive. =)

But for the 2015 generation, best to opt for the 1.5L engine, be it in Manual or AT trim.