Honeymooning in San Fran

Rick and I have been married almost 5 years. We will be celebrating our anniversary Jan 3. We have never really had a honeymoon, just a two night stay at a hotel in Tacoma. It is our goal to take a honeymoon this year. We have never taken a trip that wasn't for work or family purposes. We really just want a long, "romantic" (aka, no kids) weekend away where we can do whatever we want. We have decided that since DisneyWorld is probably out of our budget for the distant future, that we want to go to San Fransisco. Rick has been there once and I have never been and he really wants to take me. I wasn't to thrilled at first. What could be there that would be interesting? But I started doing some research and it actually sounds like a really cool town with lots of cool things to do. My top two things I want to see are Ghirardelli Square and Alcatrez Island. I know that with Rick being laid off it will probably happen a little later than hoped (not our anniversary) but it is still our goal and we are looking forward to planning it when our future becomes a little more certain. Does anyone have any tips when planning a trip to San Fran or just in general? Anywhere we should go? This is just a beginner trip. Next stop: DisneyWorld. :)