i should be clear about why my opinion is unbiased. my wife and i both drove both the yaris(4door) and the fit before purchasing the fit. now that we own the fit, when we travel we try to rent a yaris. the too clearly dominate their segment of the car market so it really was just a choice between the two.
the fit has a MUCH sportier feel all around: the brakes, the steering and the pickup at higher rpms. the fit also has A LOT more cargo room both with the rear seats up and down.
now that the yaris has the 5door, it still does not beat out the fit as you are stuck with an auto tranny. both my wife and i agree: we will never own a car with an auto tranny. the funny thing is that she is more adamant about it than i am now.
dont get me wrong, the yaris is more comfortable and gets mildly better mpg. the gauge cluster in the center took us a couple days to get used to, but definitely would not count as a strike against the yaris.
for my wife and i the fit wins and that is unbiased.
don't waste your time or time will waste you