the weather disqualified all non california cities. in CA there are only 2 real cities, SF and LA. the thing with LA is that you only want to live there if you live in the suburbs, like Pasadena. in SF one actually wants to live in the city. THen the comparison
location: the bay is the most beautiful urban setting in America, LA has some stunning mountains and wide beaches.
transportation: SF has the best public transportation system out there, LA has the best road/freeway system
weather: LA is sunnier, but the smog is horrible. SF is rainier, but very clean. They are both windy, SF has bay area wind that stings, LA has Santa Ana wind that's hot, dry and said to drive people insane.
Sports: Giants, 49ers, Warriors, Sharks v. Lakers, Kings, Dodgers and USC's football team
Character: LA's could really be found in the places tourist don't go, old hollywood is like some parts of Michigan-left behind by newer industries and newer cities (burbank comes to mind). SF isn't that much better, but they revive their older settings as opposed to bulldozing them, SF is also a bit more tech happy (think Google).
Future: LA has a grand plan, new skyscrapers, cathederal, walt disney concert hall, staples center+conplex and the like. SF has more business skyscrapers comming in as opposed to apartment high rises, the city is also investing in new industries like Biotech.
Mayors: Villaraygoza is like a CEO with a vision and a plan, Newsom is like a daring stockbroker.
Politics: SF likes power, likes money, likes daring purposals, likes social justice principals. LA likes letting people do their own thing, more immigrant based, more pro labor-i think-, and just has different morals. (Think of Catholic Church in LA w/ religious role in SF). they are both very liberal though, but different.
Schools: LA: Claremont Colleges, Whittier, UCLA, USC, Cal-Tech, Layola Marymount, Cal Poly, CSU LA, Occidental, etc... SF: Berkeley, Stanford, USF, SF State, St. Mary's, UCSF, etc...
I think overall they tie as great places, but since i'm in SF area right now, i'd give it to SF.
I was going to add Chicago, but i havn't lived their long enough to make decent comparisons.
also: My avy is off the Santa Monica Pier in So Cal.