I don't get the comment about LA? I'd say SD is pretty spread out too. The limiting factor for travel in both cities isn't distance, it's traffic. A 30 mile drive from one end to the other end isn't bad, it's the 3 hours of traffic you're sitting in that sucks.
Like LA, SD has different neighborhoods and areas. And like LA, getting from one to another during rush hour can change a 30 minute drive into a 2+ hour drive. Better figure out where you want to go and plan accordingly.
If you are into beer, you should definitely visit the number of craft breweries in the area. I wouldn't bother with a brewery tour, just drive around and visit their sites. The ones I can think of are lost abbey/port brewing, Pizza Port, Green Flash, Alesmith, Ballast Point, Coronado, Iron Fist, Karl Straus, and a few more I'm forgetting I'm sure. Depending on where you are you should visit churchill's (North County) or Hamilton's (south) and try out beer to your heart's content.
A lot of the areas of SD are defined by their nightlife. If you want to hit up bar's, SD has a pretty nice bar culture, people are generally friendly and engaging. Depending on the crowd you enjoy you can find something somewhere. Areas I can think of are hillcrest, northpark, ocean beach, pacific beach, gaslamp, and then various areas of northern san diego come up.
There is the zoo and Balboa Park. It's worth noting that the zoo and the zoo safari park are no where near each other. I wouldn't personally try to do both in one day but it's up to you. SD also has legoland, I hear it's not that great unless you're a kid or has a kid who is into it, but I've never been.
There is the convention center, so depending on when you're in town there might be something going on there, don't try to go for comic con unless you are going specifically for comic con. SD has a lot of venues for bigger established bands, and it also has a vibrant local music scene. A lot of bands have come out from SD and there are a lot of established venues for up and coming bands to play at if that's your thing. Wasn't something that I'm that big into, but there's the Casbah and Lestat's coffee shop that I can remember off the top of my head.
SD has the Chargers who play in a shit stadium, and the Padres who play in an amazing stadium. Even if you aren't a baseball fan, Padre's tickets are cheap and Petco Park is very nice and situated in downtown near the gaslamp. You can walk about and enjoy the many things in that area. The gaslamp is a bit more touristy than other places, but it's not a total tourist trap depending on where you go.
I don't know SF as well, but I would strongly say bring layers to be sure. The time I have spent there it can range from warm and pleasant to frigid and cold even though it's summer in CA. Also, if you can avoid driving, you might want to - public transportation is available in SF and works okay and i prefer it to trying to find parking, parking really really sucks in SF in a lot of places.