Mark Twain Quipped:
"The coldest winter I ever saw was the summer I spent in San Francisco."
If you're looking for warmth (having lived in both places), head south.
Having lived in both, I would take a lover to SF and stay in bed / do the warf & chocolate & chips, and friends/family to SD.
Aside from beaches/ sailing (and even this time of year it's not really that warm out (high 60's low 70's... very cold for the area, you'll see people bundled up like there's snow on the ground, so the beaches are usually deserted this time of year)... here's what's off the top of my head:
The SanDiego Zoo & WildAnimal Park are MUST dos... there's no other place like them (SeaWorld is also pretty amazing, but there are other places similar, and *much to my regret* a lot of SeaWorld has turned into an amusement park). If you have to choose... do the wild animal park. http://www.sandiegozoo.org/park/index2010
http://www.sandiegozoo.org/
http://www.seaworld.com/sandiego/
The Gaslamp quarter / SanDiego Oldtown is great fun / great dining. Drinking, dancing, music. http://www.oldtownsandiegoguide.com/
Hotel Del Coronado (Hotel Del to locals) is a must see, but check the prices before eating... often several hundred a plate.
<sniff> Fightertown USA is gone (Naval Airstation Miramar is now USMC and Topgun is moved elsewhere), but there is still a large military presence in San Diego & Surrounding. Depending on when you go there are airshows, base tours, ships & subs, and just general carousing or parades etc. surrounding the military. Check your dates, it's usually fairly well known when the fleet is returning in whole or in part, depending on your inclinations you might want to aim for or aim to miss those dates. For great eyecandy, however, any bar within 15 minutes of Coronado, Miramar, Pendelton will have an embarrassment of riches for "people watching". You'll find Marines & Sailors off duty everywhere, though. The dead giveaway is that they are required by law to tuck their shirts into their pants and be wearing belts (they often wear hats, but obviously the USMC "fade" is rather distinctive).
BALBOA Park is our nation's LARGEST entertainment complex with over 15 museums / culture arts programs, including the SanDiego Zoo. http://www.balboapark.org/
If you feel like a chatty drive, the missions are a great trip. San Juan Capistrano is THE mission to see. It's closer to LA than SD, but it's still just a couple hours up to it. http://missionsjc.com/
To know about BOTH:
SD it's our "spring" because of the cool weather and rains. Everything turns bright green with the rains (SoCal really only has 2 seasons... a very long summer and a brief spring right in the middle of winter). I'm in wet old Seattle right now, so I can't tell you what color the hills are currently... but if you're expecting gold, you may or may not be quite surprised. SF is c-c-cold (40's...just cold enough to get into your joints) and foggy damp with rain off and on. They aren't *quite* into their "spring" yet, but it would look like march/april to most of the rest of the country currently.