We were just down in San Diego, a few weeks ago. I think your wife might enjoy the Seaport Village. She could do plenty of looking around or shopping in the Village, and there are lots of things around the village that you could photograph. The village is right next to the water. There is a huge marina there too, with lots of boats. They also have a 120 year old merry-go-round. I asked permission to take photographs, and the gentleman running the ride gave it to me. Had the best fun taking photos while riding the merry-go-round.
The are some unique shaped buildings like the Marriott, and a very charming wooden structure that extends out over the water. The seagulls loved sitting on it. There is also a nice view of the Coronada Bridge.
If you want an absolute awesome view of all of downtown San Diego, have lunch or dinner at the Mister A's restaurant. Make sure to make reservations. This is no fast food type restaurant. It's expensive, but the food is good and the service impeccable. We attended a business lunch there. It is on the 12th floor.
I had never been there before, so checked out Mister A's website beforehand. I took my smaller camera with me, and it turned out that our group was the last one there, at the end of the lunchtime. I asked permission to go out on the balcony area, to take photos. They were kind enough to give it to me. With this type of restaurant, there is no way I would have attempted to take photos, without first having their permission. It just would not have been appropriate.
The view from the restaurant balcony would be perfect for a panorama view. You can see all of downtown, the San Deigo Airport, the bay, etc. As I said, it's a spectacular view. If you want to shoot from a very unique location, while at the same time, taking your wife to a place where she will feel like a queen, Mister A's is the place to go. You can check out their menu ahead of time online, which I found very helpful.
Double check on being able to photograph there though. I would not have taken photos, while others were there enjoying their lunch. We literally were the last ones in the place, and that may have had something to do with why they gave me permission.
San Diego also has a red trolly system that you might enjoy. It isn't expensive and will take you all over. San Diego is a very pretty city.
The only shot I missed that I wish I would have gotten, was downtown at a stoplight. While at the stoplight, I happened to look up, and every single building from that viewpoint, had an American flag on the rooftop. Would have loved to have gotten that shot.
Enjoy your trip.
http://www.sandiego.org/plan-your-trip/transportation/trains-trolley.aspxhttp://www.bertrandatmisteras.com/