If you rent a car, don't get the PT Cruiser. It is not what Californians drive, i don't care what the guy at the counter says.
I'm guessing you'll be staying downtown? (The Zoo is downtown)
Make that a whole day trip. The Zoo is located in Balboa Park which has many museums too, you will want to check out a few of those, especially the Aviation museum. A great place to have dinner in Balboa Park would be the Prado. One thing nobody tells you, is that the Zoo is built on a hill, so wear tennis shoes and not flip flops for sure, cus its a lot of hiking, up and down.
The Gaslamp District is where Petco Park is located. You should be able to walk up to the outfield fence (the park in the park is usually open during the day for free) and see everything. Its just minutes from the zoo. 4th, 5th and 6th avenue is where it is at. Great Shops. Lots of late night dining for any budget, and lots of alcohol too. Its usually a little bit older crowd also, late 20s, early 30s type of thing, so you don't have to worry about some 21 year old throwing up on your shoes. That would be Pacific Beach.
Minutes from there would be Seaport Village. It is a bunch shops lining the harbor with a few restaurants and an aircraft carrier you can hang out in. Def worth a visit. Across the street is the BBQ joint from Top Gun.
If you want to get out of the city, there is always Mission Bay (jet ski rentals?) Seaworld, or La Jolla (restaurants and shops on a cliff), the Wild Animal Park, Indian Casinos. Heck, Big Bear is a couple hours away if you want to go snowboarding. The desert is this kinda cold this time of year, and no matter how many times people suggest it, you do not want to make the trip to Tijuana (30 minutes). It's just a border town, it's not real Mexico, and it's depressing.
when you coming?