San Diego Zoo is huge, especially if you're into zoos and plan to explore the whole thing. If the only thing you do is take the bus, you may cover a lot of ground but I don't think you'll see all the exhibits.
I've never been to Seaworld, but I'm not sure I would recommend both in one day (especially if you have young kids). My wife and I did some walking around the Museums in Balboa Park after doing the zoo and we didn't stay long. Of course, this was on a hot summer day in August; I'm guessing the weather will be much more temperate in December.
P.S. I would consider getting a rental car -- they're usually pretty cheap, and it's much more convenient than taking the bus and/or subway everywhere. Parking can be an additional expense, but the time you'll save is worth it IMO. As for traffic, stick to the main streets rather than the freeways and you'll be fine. Are you driving down to SD?
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