I ended up choosing the Pacific Shores Inn for a business trip in June 2007, as it was the only the only reasonable place available in the area. Enroute to San Diego, I was trying to lower my expectations, as I have learned not to excpect much from beach motels. However, I found this place to be quite a gem.
My recently remodeled room (I can't speak for the other rooms) had a comfortable new bed and a beautiful, fresh decor that was on par with what you would see at an upper-end Hampton or Fairfield. The staff was very friendly and professional, the heated pool was petite but pleasant, the rates were great ($110-$130 per night), and the 1/2 block walk to the beach made this place a winner! This place shouldn't be mistaken for a "business hotel" (unless your business is surfing), but it made my business trip seem more like a vacation.
The only downsides I could see were the "continental breakfast" (just a box of doughnuts/danishes) and the potential for the street noise to become more of a problem than in your typical thin-walled hotel (especially in room close to Mission Blvd).
Currently, less than half the rooms are recently renovated (all should be done by summer 2008), so request one of those and you should be set up for a great, "affordable" beach vacation.
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