My CA friends are constantly astonished at my preference for Chicago over SF, but that is simply because they haven't been there to see it themselves... yet! I have lived in both cities for multiple years during my 20s. Here is my experience:
SF upside
SF is a great place. In my mind, this is primarily because of its progressive approach to worldly concerns like the environment and social issues, and for its role as the world's center for technological innovation. For residents, SF is a great home because it has the fortune to be placed in the best geographic region in the world. If you actively take advantage of it, on any given weekend you can visit Point Reyes, Yosemite, Tahoe, Santa Cruz, Napa Valley, Monterey, John Muir Woods, and many other one-of-a kind destinations. You can bike into the hills of Marin or go surfing (in a wetsuit) in the ocean. But what SF has to offer is largely outside the city itself, and they are only of use if you are an avid outdoors person or make frequent day-trips. If you're a city slicker like me who has been to all those places but never does more than 4 such trips/year, it's hard to accrue these benefits.
Chicago Upside
Chicago on the other hand is a world class metropolis with millions of people and the cultural, artistic, economic, sports, and culinary benefits that come with it. There are too many specifics to discuss, so I will highlight some of my favorites.
Summertime
Chicago in the summer is simply paradise. The energy, activities, and attitudes that seize hold of the precious warm months cannot be matched in other US cities, even NYC.
There's always a big and worthwhile festival happening, and we're not talking some silliness like the SF Polk street jazz fest. The city has 30 miles of uninterrupted beach-line which is often within a 5 minute walk from your office building. Chicago's motto is Urbs in Horto (City in a Garden) for a reason.
Neighborhoods and Community - Frank Sinatra called Chicago the big city with a small town feel. This is most well captured by the fantastic variety of neighborhoods, each proclaiming their own authentic flavor. Whether you live in Lincoln Park, Logan Square, Hyde Park, or Pilsen, among many others, you feel a sense of pride and community that I could not imagine myself experiencing in any SF neighborhood. I've dabbled living in many parts of SF, as well as Oakland, and the neighborhoods don't compare. Another proxy for the city's community is the Chicago Marathon. While no one seems to care about SF's two marathons (they probably accumulate less than the 100,000 spectators, a sum the Chicago Marathon achieved in 1905) the 1 million Chicago spectators that get out and cheer on runners every year with shouts, signs, and cowbells is just another testament to the city's sense of pride and community.
Food - Chicago's restaurant scene is constantly trying to out do itself. The variety, quality, and service you can find outstrips SF and at much more reasonable cost. The city also boasts addictive homegrown delights such as italian beef and Garret's popcorn, to name a few unknown outside the Midwest. A friend recently joked how absurd was the level of joy, exhilaration, and anticipation he felt upon picking up a Lou Malnati's deep dish pizza. Rushing home so that he could devour it with friends felt like running down the stairs on Christmas morning when you are 8 years old. I, and probably any Lou's customer knows exactly what he means. I would be remiss to ignore that there are 2 food categories in which SF beats Chicago: Asian food and the locally grown, organic food prep movement known as California cuisine (which is from Berkeley). One might think SF's Mexican is also superior, but very surprisingly Chicago tacos are tremendously better than SFs in part because of a recent trend of Chicago restaurants attempting to concoct the perfect taco. But SF burritos still beat Chicago's by far.
Cost of living - This is the street I lived on in 2010. It is an urban paradise, hopping with activities, restaurants and bars, very safe, a 5 min walk to Lincoln Park and a 10 min walk to the beach, and 18 min El ride to the Loop. Two friends and I shared a classic redbrick 3 bedroom, 1 bath flat with a huge living room, a dining room, kitchen, back deck, and shared backyard lush with greenery, picnic table, and lawn. We averaged $620/month, utilities included.
By comparison, 3 years later the building I live in at Polk and Pacific in SF (by SF standards a very in-demand neighborhood) starts at $3000/month for a 1 bedroom (ahh!!).
Beautiful people - Chicago has proportionally more and by a wide margin, and they're generally friendly unlike their rare beautiful counterparts in SF. That's all I should probably say on that topic.
SF Downsides
Crazy people - There are so many in SF that, sadly, residents are inured to their existence. I've witnessed a person in public screaming at the top of their lungs and a tourist trying to assist them while all the locals just went on their way. It's an issue rather foreign and strange to people outside the SF Bay Area.
Public transit - SF's Muni is pretty terrible. I've been on both buses and subways that have taken 50 min on what should be a 15 min ride. Less than half the riders pay for the ride, so you feel kind of scammed when you do the right thing and pay. SF's cable cars are awesome, but it's $6 oneway and mostly serves tourists. Chicago's transit on the other hand is cheap, ubiquitous, effective, and reliable.
Concrete and filth - SF is a dirtier city. Furthermore, despite the wider area being known for nature, it is a 7x7 mile paved sidewalk. There are no lawns, greenery, or rarely even trees lining the streets. You have to go to the parks and hills for a simple dose of green. While Chicago's magnificent mile here is strewn with artful planters boasting exotic greens (I once bumped into some Swiss chard to my surprise),
(Michigan at Superior, Chicago)
SF's Market Street is laden with dirty bricks, garbage, and the smell of urine.
(Market at Powell, SF)
(Market at Jones, SF)
Chicago Downsides
Violence and segregation - Chicago is still plagued by a history of segregation which striates the city's regions into a discrete spectrum of very safe to very unsafe. Per capita the city has a much worse crime problem than LA and NYC. 2013 has shown drastic improvements in key stats, with the murder rate at its lowest level since 1965. It has yet to be seen whether this actually improves quality of life in the most violent "hotspot" areas. (Gun violence and murder are on the decline in Chicago)
Winter - I actually love the winter and consider cyclical annual weather to be a good thing. But I know some people avoid freezing temperatures at all costs so it's worth mentioning here.
Conclusion
On the whole if you like cities and don't mind winter, Chicago is simply the best. If you go on amazing bike rides every weekend, SF is your spot.