If you are talking about PakSuzuki, which probably you are, then apart from tech differences, the size of engine matters too. So, if one is using old beaten up Mehran and is getting heating issues while other one is using old worn up Honda City and he is good to go then it is because of the differences in price, engine size and the category of the car.
You just can't compare companies like that but yes, Honda makes very good engines and that's confirmed. Toyota is very good at it too, we all know about Corollas, not sure of Suzuki, as Suzuki mostly make smaller engines in bulk having low prices. So you have to give in something to keep the price down.
Also, Suzuki make cheap and affordable cars for masses while it is not usually the case with Toyota and Honda, Suzuki mostly focuses on smaller segment cars while the other two try to cover all segments.
And Yes, Honda and Toyota make quality stuff when compared to Suzuki as Suzuki is not for luxury it is focused on affordability even Toyota and Honda are not for luxury either but we are forced here in Pakistan to consider them as Luxurious Vehicles while Suzuki as a 'good small car assembler'. (It's a long debate)
You should have mention the PakSuzuki cars, you have driven, in which you faced heating problems as even in Mehran after the euro 2 introduction, not many people report of heating problem, if driven with care.