I don't think it's a valid comparison brother.
Yaris is a CVT, bigger and wider in size, has modern safety features, airbags, traction control, Toyota's comfortable suspension, climate control etc.
Current PKDM City shouldn't be compared to it. It's a very old generation, no modern features, stripped out all of them. Hard suspension (but some prefer it too).
When Honda launches the next City, that will be the right competition.
But if you want to wait 2-3 years, sure. If you want to purchase now or in next 1-2 years, the choice should be Yaris.