Often, you'll end up emphasizing either the comparisons or the contrasts in this sort of essay. So, you might say "City A and City B are both superficially similar in that they possess characteristics A, B, and C. However, they are really quite different because of characteristics D, E, and F." Whether you end up emphasizing the similarities or the differences depends upon which of the two are least obvious, as it is more interesting to argue that two apparently similar things are different or that two apparently different things are similar, than it is to say that two things that seem the same mostly are similar, or that two things that seem different actually are different. As most people choose two apparently similar things when asked to write a comparison and contrast essay, that usually means that you'll want to play up the differences.
Sean, EssayForum.com