I used to take my daughters to UCSD pediatrics when they were located in Hillcrest, but a few years ago they moved up to the Rady's Children's Hospital campus, which is far from me. It was a big practice and we rarely saw the same doctor, but all the doctors were great. We didn't do any vax at that time and never felt pressured by them, they were always supportive of our vegan diet, and they were caring, took time to really talk to my kids and assess their development. I was really bummed when they moved. That was a number of years ago, so can't vouch for them now, but is definitely worth a look. Here is their website: http://peds.ucsd.edu/generalpediatrics/about/
Now my kids see Dr. Hibbs at this practice: http://peds.ucsd.edu/generalpediatrics/about/
They aren't affiliated with UCSD hospital, but do take a lot of insurance companies. This office is often recommended, along with Dr. Barr, as the most crunchy-supportive pediatricians around here. Most of the midwives at UCSD take their kids to Dr. Nakahara, a colleague of Dr. Hibbs. The only thing is that it's another big practice and dealing with triage can take a long time. I just keep bugging them until I get an answer/ appointment. The doctors are great, except for Govendor, who just does the evening hours, everyone I know avoids her like the plague, but it's pretty easy to get appointments with other doctors so I don't hold it against them too much.