Some parts of SD economy are in trough at present, but other parts are not.
Heavy construction is very strong. Bio – stem cell funding from prop 71 is about to get flowing. A/E community is fairly busy. Many big project working their way thru planning ( eg hugh Marriott by ballpark ). Pendleton has large amount of allocated $$ for buildings, ditto Navy at 32nd. Bio conference has many job openings for SD area.
Are there problem areas – absolutely yes, but compared to alot of the rest of US we look in pretty good shape. Not every area obviously such as Eastlake, Vista, San Marcos and others that can be named, but lots of other areas are becoming more stable abeit at a lower level than 2005/2006. So choosing the area is most important.