San Diego has some of the best weather in the entire US, and being right on the coast, and a downtown that is adjacent to water, it has tremendous assets that other cities just can't match. It's interesting that until recently, downtown San Diego has done a pretty incredible job of cutting itself off from the amazing asset; it's waterfront.
It's perhaps not entirely fair to blame San Diego's waterfront woes only on the city. The city has a rich military background, which took up a good portion of the waterfront. Even today, as the city moves forward with large condo towers, there are several stout military buildings (and their respective parking lots), littering the space between downtown and the water.
It would however also be unfair to not blame some of the issue on the city. In the late 80s, the city opened the massive convention center along the waterfront. The building, which doesn't utilize any of the assets of being on the water, goes a step further, by creating a huge, impenetrable wall to keep residents of the city from making their way down to the water.
The connection between downtown and the water is also impeded by numerous large blocks, where the regular street grid is abruptly intercepted by buildings that stop the flow of foot and auto traffic. There are some blocks that allow for pedestrians to continue on their way, but without the flow of cars, the restaurants, cafes, and other shops that make for a successful pedestrian environment are gone.
There have been some steps to improve, such as a new walkway path between downtown and the waterfront next to the Mariott, but adjacent to this is a new parking lot sitting directly on the waterfront. There are also proposals, which hopefully won't go anywhere, of putting a new Chargers football stadium near or at the site of the current Seaport Village. I'm certainly not against updating the Seaport Village area, but am against another large barrier that sits vacant 95% of the time and cuts citizens off from their waterfront.
San Diego likes to tout itself as America's finest city. Perhaps if over the coming years it can connect itself better to it's waterfront, it may at least have a chance of living up to that moniker.