Berkeley Review by a mile. I was asking that exact same question last year about this time (right after winter quarter registration). I was actually leaning towards PR, because I was under the impression BR didn't have CBTs. It ends up they have CBTs that are really good. And their teaching is so much better than PR that I'd have chosen them just based on the teaching. The fact that the BR books and tests are better than PR was just gravy.
You ask what makes a difference besides teaching, and I think teaching is the biggest factor that is far more important that anything else. You can buy exams and books anywhere, but the one thing you can only get from a class is quality teaching. After having sat in on lectures for both classes, I found the teaching style much, much, much better at BR. What I liked is that they taught how to take the exam and gave us great strategies and tricks. Instead of giving us equations, they showed us how to use the equation to grasp the concept easier. I was able to go right from lecture and do really well on questions. I think the fact they only teach MCAT makes a huge difference in how they teach the class.
If you have the time, you should sit in on lectures for both classes. You can look at the books, but honestly I wouldn't know which was better without actually working through them completely. I just trusted people at SDN, because it seemed like everyone who had all the different books concluded the same thing: BR for physics and g chem, EK for verbal, EK for bio, and BR or EK for o chem depending on your background. After working through three different materials, that's my conclusion too.
Good luck with your choice. Having been through it and having gotten a score better than I was expecting when I first started, I'd say BR over PR in Westwood is an easy choice.