Well, just with the brand alone, you can have assurance when you buy the honda as a new unit and with the after sales service.
My beef with the 1.3 engine is that it feels weak to pull the cars weight so accelerating seems harder for this vehicle compared to the previous generation, even though it was an i-DSi and not VTEC. Plus the price seems a bit too high for what you can get if you are really looking at it.
At a price of around 750k, you could get a compact sedan, instead of a sub compact. Namely the Ford Focus just by adding around 50k to the budget. This would be a good car especially if you plan to take it on long drives from time to time plus you got a bit more room in your vehicle for "stuff". But again, you may just want a city car and the fuel efficiency maybe the one at play which is why you considered the 1.3 MT of the Honda City.
On short stints, we only got around 8-9km/l on our old 1.3 Honda City (similar to the current gen engine) for exclusive city driving. On the i-DSi Honda City, we also got roughly the same fuel economy but it was more responsive an engine for us compared to the current 1.3 engine.
Since you are opting for a manual, then I think you could consider the 1.4MT of the Ford Fiesta not the AT Model (hate the transmission while we wait for the update to the compubox). Up to you if you want to consider the 5-dr or 4-dr. It can fall below your budget for the City 1.3MT so you may have accessories put in to change "stuff" you may want upgraded. =)
As for the Rio, now that is certainly a looker. Again, I just have hesitation, not with the build quality when it comes out of the factory but with the after sales service of Kia Philippines as well as parts availability. This has been an issue with them for how long yet I do not know if they have resolved this or not. So I can not update you with the current performance of the after sales service. But the car itself looks like a great buy as well. =)
Good luck in you purchase. Cheers!