Stayed at the Westin, back when it was the Omni, right next to Horton Plaza. Great place, very convenient and a great pool area. Read reviews of construction noise recently, but they should be done by summer.
Hilton San Diego Bayfront, back in 2006 they had shuttles running out there, so made it a lot easier to get to the center and back. Great views across the bay to downtown and North Island base, usual excellent room/staff as Hilton should be doing.
Chula Vista Bay Breeze, would not repeat, a little dumpy with a lumpy mattress.
South of the border stuff:
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Login Stayed here for a couple nites in the past, but I work in a trip to visit a friend who has a house in Mexico, so crossing the border isn't a problem for me, just time your return back to the states so you aren't trapped in the commuter traffic.
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Login Wife and I stayed in the Bali Suite here, had a 22 buck a nite deal on a Wednesday before their busy weekend traffic. We go back about twice a year, weekends aren't easy to get; would compare this room to a nicer room at the Disneyworld resort, somewhere between the Swan/Dolphin and the Port Orleans.