Just stumbled across this thread, but as a UCSD graduate and San Diego resident, I thought I'd chip in my thoughts in case it's still helpful.
First, if she's going to be at UCSD, the UTC area, close to campus, is where I'd look, especially over downtown. Traffic on the stretch of I-5 between downtown and UCSD is opposite of what you'd expect, the morning commute is congested northbound (away from downtown and towards UCSD) and the afternoon commute is congested southbound. So if she's commuting from downtown, she'd be driving in traffic. Also, investigate the cost of a UCSD parking permit. They're not cheap and supply of parking spaces is limited.
If you find a place in UTC, she may not have to drive to campus at all. Between UCSD's own shuttles and the MTS bus routes (in particular, the SuperLoop routes), bus coverage between the area and campus is pretty good.
UTC (the name specifically is a shopping mall, but I use it to apply to the surrounding area as well) has tons of apartment and condo complexes. When I was looking I just went around and talked to the various leasing offices in person and got their info, but that's obviously difficult to do if you're back in Boston currently. I'm sure you can do lots of online research.
Other areas to consider would be University City (south of UTC), which has more single family homes but might have options for renting. Further south is Clairemont Mesa, which is less expensive than University City but not as nice. In either area, if you are close to Genesee Ave, there's still the possibility of decent MTS buses to get to UCSD.
Another option would be to go east into Mira Mesa. There are both homes and apartment complexes scattered around, though some areas are nicer than others. Bus to UCSD is possible, though it can be a little slow. MTS has a proposal for a new "rapid" service between Mira Mesa and UCSD that would help there; it would be quicker because it would make fewer stops.