To WonkaNerds/livinsunny,
First off: congratulations. You are both in the driver's seat, clearly interviewing at great programs. Save for the bottom half of livinsunny's list, neither of you is going to have any problem matching into a strong fellowship. So my biggest advice would be not to overly stress about this and not to try to parse out some tiny difference between the programs, and instead go based on the place you liked the most when you visited, where you'd like to live, etc.
I am an intern at Stanford, so I was obviously in your shoes last year. Of the programs you two listed, I interviewed at Stanford, UCSF, UCLA, UCSD, Northwestern, U. Chicago, and BIDMC. I had a pretty strong preference for the west coast. Despite my advice above, I too stressed about the decision, and in the end decided to rank my top four as Stanford-UCSF-UCLA-UCSD. I had a hard time (especially with the top 2), but I liked my day the most at Stanford and felt that these were the residents I liked the most on the interview trail. I also slightly preferred Palo Alto to San Francisco, which I know is not the case for everyone, but was for me. I decided that I would really have equally strong options for fellowship afterwards, so I should 'go with my gut' which in the end pointed me to Stanford.
I have had a great year so far, and would certainly make the same decision now if I had to do it over again. It sounds like when the PD change happened a couple of years ago there was some unhappiness from some of the at-the-time current residents, but I can certainly say that none of that is the case now and people are really happy and very well supported, and the environment here is one of the real strengths of Stanford. I imagine that I would have been really happy at UCSF, UCLA, or (likely) UCSD as well, but this is just where I felt the most at home.
So again, I'd say to recognize that you guys are going to do really well no matter what, so just choose it based on where you had the best feel, which residents you felt you would most like to work with, and where you'd want to live. You're very unlikely to go wrong.
Specifically for livinsunny's list, and taking into account that you want to live in California, this is how I'd do it -- but again, don't go with what any of us say, go with what you feel.
Stanford
UCLA
UCSD
U. Chicago=Northwestern=WashU=BIDMC
The rest
Good luck to you both.