Based on your comparison, if the budget within Myvi 1.5 range, the Vios and Altis probably second hand with the Altis even older '03?. I would go for Vios or Altis anytime over milo tin Myvi. Altis & Vios are technically proven most reliable though handling wise, none of them are good. Torque and power all go to Toyota.

If you wanted to go for the old Altis, you can still keep driving it as its reliability is good enough to last for few years more before require overhauling. Overhauling the Altis engine totally would cost around RM4000 for inline4 engine if done at Toyota SC. Do outside, will end up getting conned instead. Terbalik when comes to overhaul.

Number of cylinders is main factor in determine the price of overhauling, not the engine size.

Outside workshop, you'll end up easily conned on the markup spare part price, labour & no guarantee that they really but the new part for you (ori, OEM or imitation?).

SC, whatever they charge, they have the guide and the fixed price to follow. Since more parts are involved, better do it at proper SC and make sure that SC is a big one with more technical knowhow around. Smaller SC or ciplak SC with irresponsible technician could also cause headache.