Princess Amy -
Don't worry about staying at the Good Neighbor Hotels. One of the differences between WDW and DL (in my opinion) is that in WDW you are totally *in the bubble*, and it adds so much to be staying onsite. At DL, you really don't have that bubble, just because DL is located in the middle of a city! Although the Disney hotels are wonderful, and I love to stay at them, the theming isn't quite as pronounced as WDW, and you really don't lose any atmosphere by NOT staying onsite. Plus so many of the offsite hotels are just as close to DL, CA and Downtown Disney as the DL resorts!
If you are coming out for two weeks, there is so much to see and do in Southern California - SeaWorld, the San Diego Zoo, Legoland, Universal, and the beaches. If by staying at the Good Neighbor hotel, that means that you can do that much more, than totally worth it!
If you really feel that staying onsite would add to your trip, maybe stay a week at a less expensive hotel, then go down to San Diego for a few days, and then end the trip back at Disney, staying on site for just a couple of days - that way you would get to experience everything!
Good luck!