Great Location
The Holiday Inn on the Bay faces the San Diego Harbor. Directly in front of the hotel is the Star of India (Maritime Museum). 
PLUSES:
1. The hotel is conveniently located to the cruise terminal. It would be an easy walk provided you do not have too much luggage. There is a cruise parking area located very close to the hotel.
2. The hotel offers a free shuttle to the airport, seaport village, Horton Plaza, and Balboa Park (leaves at 9 or 11 AM and returns at 4:20 PM).
3. The rooms are large. The room we had was remodeled and included a large walk-in shower (no tub), king size bed, chair with ottoman, desk area, dresser and large flat screen TV. Our room was clean and odor-free.
4. The H.I. restaurant (Elephant & Castle) has a good happy hour ($ 4.50 beer/wine/mixed well drinks) from 4 - 7 PM. There is a wide selection of beers available. 
MINUSES
1. Parking (self or valet) is expensive. Neither parking area is fenced or secure.
2. Rooms facing the bay have a lot of road noise. North Harbor Drive is a busy road and the traffic can be heard all night. Rooms that face to city have the train tracks close by so you hear the train whistles and the railroad crossings. 
3. The hotel is actually three buildings. The front building faces the harbor, the back building is a multi-story (lower floors face the front building, upper floors face the harbor or the city.)
4. There are limited places to eat within walking distance. A Ruth Chris Steakhouse is next door; a Denny's is 2 blocks away (but you have to cross a busy street to get there).