I've owned the Yaris since it first came out in July of 2006. Mechanically speaking, this car has been perfect. Never had a problem with 45k miles on it. That being said, this car has serious faults in other aspects. 1) The interior quality is abysmal. I've had a dash rattle for 3 years now that 3 dealerships have been unable to fix. My window roller broke within 3 months, and the trunk has had issues with sounds and closing. 2) This car failed me in the snow, spinning out and nearly getting seriously wrecked. 3) Over time you feel claustrophobic in here. 4) Jumpy acceleration is unpredictable from a stop, sometimes hurting my neck, or almost hitting other cars. 5) Serious lack of power.
Mechanically this thing is perfect, so you don't waste time/money on maintenance. If you are driving on level pavement, power is adequate.
Better quality interior build, fix the crazy acceleration, how about power windows and door locks on the S model, what the heck did I pay extra for? Stability control would have been useful.