I am having the same problem. What IS it with commute time and this game? Houses always abandon in my cities and it stops me developing them. I have tried everything; bus stops on every corner, subway networks, avenues and highways etc.
I have even experimented with road networks - like laying them out in a grid of avenues which disperse into smaller roads and streets, as well as both reducing and increasing the amount of crossroads traffic has to go through. I have also tried a winding road pattern found in some European cities, but still the amount of 'abandoned due to commute time' buildings is astronomical! And also, no matter where you put industrial and commercial zones, sims still won't travel to them! I have tried putting jobs in the same square as the residents, and over the road, with several transport links such as buses. I have tried isolating each individual zone, so only the same type of zone is found in that particular area. But the no job sign still appears! And the strange thing is is that it's almost certainly always the wealthy sims that abandon, even though the jobs in the city are mostly high-tech and Co$$$ commercial!
I've tried building a city primarily of low-density zones (as i thought the problem was caused by too much traffic on the roads)but by the time the population reaches 30,000 almost EVERY wealthy house has a no job sign above it. Then all the buildings either distress or go black which makes the city look awful.
I have also tried altering the amount of cities joined to it, and the education and the amount of jobs found in those cities. But no matter what it never makes a difference. Education and health in the city are all really good, as is the road traffic. Crime, air pollution and fire-risk are low. Is it all just to do with the 'bug' found in the came? If not, how are we supposed to overcome this ridiculous problem?