I just graduated from Berkeley undergrad this last May, with a major in Molecuar and Cell Biology. I'm entering UCSD (which I chose over Berkeley) this September for grad school as well. I've done some real thinking regarding the two places in regards to grad school, and think I could be of some help.
-Living-
I've experienced the Berkeley area extensively, and visited UCSD a handful of times. Definitely Berkeley/SF/Bay Area is a much more condensed, metropolitan, and "happenin" place than La Jolla. Of course at UCSD you could go to the Gaslamp district or downtown SD or Pacific Beach among other things. But in my opinion nothing beats the college town atmosphere that you'll find at Cal Berkeley. Of course Telegraph avenue does look ghetto at first glance. But amongst the transient population and the hippies, there are some real gems when it comes to coffee shops and restaurants at Berkeley, all within walking distance from the campus. I believe the atmosphere there is a lot better, especially for a college student. On the other hand SD definitely has a car culture, where you won't be able to do much without your own car. I wouln't know much detail about what there is to do at SD not having spent too much time there, but I must say that the impression I have now is that I would miss the atmosphere up at Cal. Rent at both places is exorbitant. =\
-Academics-
I must disagree with the previous poster who stated that Berkeley does not have a good reputation in the sciences. It's common consensus that Berkeley is amongst the best universities in the nation when it comes to science, particularly physical sciences and engineering. The graduate programs rank consistently in the top three amongst places such as Stanford, MIT, and Caltech. In the biological sciences, they're still pretty darn good. Competing with other universities such as UCSF, UCSD, Johns Hopkins, Stanford, etc. Of course I'll admit rankings aren't something you should base your decision upon. But my point is, for the sciences, Berkeley is one of the TOP places to be, both in the public's eye and reputation among the academic community. Cal is VERY well respected.
BUT, a majority of the innovation and high profile research at Berkeley (and in SD) is on the graduate level. Obtaining a world class undergraduate experience IS possible at either university, but its up to you, the student. Interacting with top notch professors requires a proactive approach. I have many friends at Cal that are lazy and just breeze by with C's and the minimum effort. Doing so is still possible as there's very little individual attention in such a huge undergraduate population as Berkeley (or SD). So you WILL run into slackers, stoners, and burnt out asians that got pushed too hard in high school and now just want to watch anime 24/7. But the majority of the population at Berkeley is very bright. I don't have extensive experience with UCSD undergrads, but what I hear from a few undergrad friends there is that its very much more laid back.
That being said, I believe its somewhat safe to generalize that Berkeley has a much better repuation than UCSD on a school-wide context. In the area of Biology, the gap is a lot finer, with both schools having areas that they excel in. SD is top notch when it comes to neurobiology, Berkeley better in biochemistry and structural biology. Furthermore, I believe its also safe to generalize and say that Berkeley has a more competitive and "high achieving" undergraduate population than SD does. To the OP, this may translate to having more clout when applying to med school. A 3.7 GPA, may in many cases look *better* from Berkeley than it would at UCSD, where the competition is substantially lower. Trust me, Berkeley premeds are INSANE. But...med schools love 'em.
Having said that, the best bet is to visit both campuses and see what fits you best. Yes, my belief is that Berkeley is a better choice due to the college town life, and the substantially better university reputation. However, if you end up hating it there, or getting stressed to a point where you can't excel in your classes, there would be no point in going there over SD. UCSD is by no means a bad choice, especially if you think you'll enjoy the atmosphere there over Cal. Regardless, I don't believe you should live at home unless for financial reasons. You'd be missing out on a huge part of the college life if you lived in SF. Plus you don't wanna BART every day do you?

And yes, SD has great biology programs and nice new facilities, but I think these matter more on a graduate level. Most undergrads focus on class requirements, getting good grades, having some fun on the side, and doing some undergraduate research in a lab. It doesn't matter too much that SD has so many private partnerships, receive X amount of money for stem cell research, spend X dollars per year on alzheimer's etc. because an undergrad wouldn't be able to take advantage of it as much. But this is why I personally chose SD over Cal. I felt that there were more cutting edge opportunities in the medical/biological field at SD on the graduate level.
I think my post is long enough, though if you have any more questions, feel free to ask, as I've just finished making my own decision not two weeks ago.
:edit: One more thing: one of the previous posts metioned lack of attention. I think this is one thing I forgot to stress. There are 20,000+ undergrads at Berkeley. So personal attention is NOT something you'll receive. I went though my undergrad career there and saw my "advisor" twice. For five minutes each visit. I never met any deans or got any acknowledgement of my existence aside from being issued a student ID number. So if this is a problem for the OP, it might be something to consider. Being premed, you very well might major in Molecular and Cell Biology as well. And that I believe is the largest department on campus, so this problem is even further exacerbated. So: persistence, independence, and proactiveness are all qualities you would need to succeed at Berkeley. Of course I would imagine this is true for UCSD as well.