I don't really have any hotel recommendations, but I have a bunch of activity ones.
I second the zoo and pretty much the whole Balboa Park area, which is where the zoo is situated. It's gorgeous, extremely walkable, and there's a ton of museums and gardens there. Balboa Park offers an explorer pass which will get you into 17 participating museums there. Depending on how many you hit, it can definitely be worth the money.
I also second La Jolla Shores for swimming and La Jolla Cove for the seals. There are some remarkable views there. If you're feeling up to it, you can take advantage of the kayak/surfboard rentals.
While In & Out is a west coast staple, if you really want a fantastic burger and don't mind going a little out of the way for it, go to Hodad's in OB (Ocean Beach). It's a San Diego institution. There's also a Hodad's downtown, but the area it is in is kinda sketchy. The area it's in in OB is funky, and on Wednesdays from 4:00 - 8:00PM, they have an awesome street fair with bands. It takes place literally just a few feet up the street from where Hodad's is located.
The Gaslamp Quarter is super lively and there are some great pubs, bars, clubs, and restaurants there. Our favorite place to go there though is The Shout!House. It's a dueling piano bar. The piano players take requests and can play anything from classical to rap to current chart toppers. They also play Disney and Nintendo music from time to time when requested. They do get a bit raunchy as the evening wears on, but if you don't mind that, it's a fun place to go and I recommend it.
If you stay near the ship, you'll have the San Diego Waterfront Park to explore. Little Italy is just up the street from there and has some delicious restaurants as well. You can also tour the Star of India or if you walk a couple blocks south, you can tour the U.S.S. Midway. There's a fantastic side park next to the midway with a bunch of different memorials to our servicemen and women, as well as the giant sculpture of the sailor kissing the nurse in Time's Square at the end of WWII. It's called the "Embracing Peace" statue.
If you continue south that way, you can walk to Seaport Village, the marina, and the Convention Center. If you want to hit an infamous movie spot, the Kansas City BBQ is across from Seaport Village. If you've seen Top Gun, that is the place Maverick and company sang "You've Lost That Loving Feeling". I've never eaten there, so I can't say how good it is.
You may also like visiting Coronado, which has a lovely beach, fancy houses, and is home to one of the inspirations for Disney World's Grand Floridian, the Hotel Del Coronado (or Hotel Del, as we locals call it). You can get there one of two ways, but the quickest would be using the Coronado Bridge, which is the giant arching blue thing that stretches over the bay from downtown to Coronado.
And a few other suggestions for around here:
- If you like baseball, Petco Park is a trolley ride away, next to the convention center. The Padres play there. You'll have to check their schedule to see who they're playing but it might be a team you want to see.
- Point Loma's Cabrillo National Monument and Liberty Station. The Old Point Loma Lighthouse is open to visitors at Cabrillo and there are some breathtaking views of the Pacific. Liberty Station isn't too far from there and houses some great restaurants.
- If you're up for exploring more of San Diego county rather than just the city (and you have a rented car), Del Mar is worth a visit, as is making the drive to the mountains to see Julian or visit the observatory at Palomar Mountain. If you'd like a taste of the Old West, there's Old Poway Park in Poway or Old Town (which is touristy but it's also fun and has some museums there). Head to the glider port in Torrey Pines to watch people take off and hang glide over the beach. There are also hot air balloon rides, if you're feeling adventurous. Torrey Pines also has some great trails. And if trails are your thing, you should definitely hike to Potato Chip rock. For those with hiking experience and who like a challenge, you should take the Lake Poway trail up. For those who aren't interested in an 8-mile round trip hike, use the Ramona side trail. And you'll want to take your picture once you're up there to prove you've done it.
- If you'd like to see the sister park to the San Diego Zoo, you'll need to visit the Safari Park (Wild Animal Park to locals) in Escondido. It's a different experience from the Zoo and they offer a lot of different adventure/interactions that you can't get at the Zoo. For instance, there is a caravan you can take out into their open roaming grounds and you can feed giraffes. They also have a zipline and ropes course that puts you high in the trees above exhibits and people. You can also sit front and center during a cheetah run demonstration and meet the cheetah and her pet dog after the exhibition. Even if you don't want to spend the money on the different adventure/encounter packages, you can still get up close with a lot of animals there through other exhibits (like the lorikeets, lemurs, and butterflies).
- For Mexican food, Lucha Libre is supposed to be fantastic. I've never been, but every time I've driven by there, there is always a line out the door. El Indio is supposed to also have terrific Mexican food and is just a block away from Lucha Libre. My favorite place in that same area though is Shakespeare's Pub. It's an English pub owned and operated by ex-pats. They also operate a little shop around the corner that sells a bunch of British goods, from food and drink to dvds and teapots. We always hit it up afterward to stock up on our British candy and crisps. Then there's Hillcrest which is home to a lot of delicious restaurants, like Snooze, Hash House-A-Go-Go, and Bronx Pizza. For sweet stuff, you might want to hit up Extraordinary Desserts in the evening and Donut Bar in the morning. But you have to get to Donut Bar early because they sell out quickly and once they're out, they close for the day.
- San Diego is the nation's hotbed for microbreweries. If you like beer and are interested in taking a tour, many local breweries offer them.
And while I can't speak of the buses, we love the trolley. It's easy, convenient, and not that expensive. Definitely make sure to purchase your pass though; they check often to make sure you've paid to use it.
Hope that helps!