Is it just me or are schools extra-suspicious of people with very strong academic backgrounds? The repeated hobby questions you got almost suggests that they think having a high GPA is indicative of some social shortcoming. If so, that's completely unfair. If anything, a strong GPA should be a benefit, not a liability. UCSF brags about regularly rejecting 4.0 students for "lacking experience," and it sounds like UCSD is following that trend. 😡
Asking the admissions committee for an explanation for your rejection sounds like a good idea. I don't know who specifically you would talk to, but e-mailing the dean would probably work. If he's not the right person, he should be able to forward your inquiry to the appropriate party.