ybc your question is a bit to general. The best neighborhoods will vary for all of us due to taste and other priorities. The best neighborhood for a young single person who likes the bar scense is most likely Pacific Beach or an associated area. The best area for people with young children may be an area with excellent school districts. Still other people may want an area with large lots and spread out homes.
What is important to you? I have been in San Diego for 25 years now and I know all of the areas very well. Are you looking for a good school district? What part of town do you work in? Do you want a home or condo? Specify a bit more what is important to you and I bet you will get lots of information from the regulars here.
As for builders I am not as qualified as some of the other people here who have a great pulse on many of the new developments, especially in Carmel Valley.