A few months ago, I updated a city rating system (available at http://lewyn.tripod.com/livable09) that evaluated cities' "livability" by rating crime rates, transit-friendliness, and cost of housing.
Plenty of cities did very well on the first two criteria. For example, New York is now safer than most big cities, and of course is by far the best city in the U.S. for public transit. But its housing costs are dreadfully high. The same was true of Boston and San Francisco (which, if only crime and transit were considered, would rank second and third for livability).