The Vios has better fuel consumption (by about 1 km/L in city driving). It's also cheaper to maintain, especially outside the casa. More practical, but less exciting too.
Cash discounts are abundant (60k ata yung standard discount ngayon), unlike the City where you'd be hard-pressed to get even just a 10k discount.
Space and legroom, eto napansin ko - the Vios is a smaller car, but for some reason, it feels spacious. I think it's because it has narrower front seats, but bottom line, given identical front seat positions, the rear space of the Vios is actually decent. The City is a bigger car so naturally you'd expect it to be more spacious, but the difference isn't that big.