I'm a full time professional chauffeur in San Diego and knowing the quality hotels in the area comes with the job. There are tons of very, very nice hotels in the area, but there are two in particular that I want to stay at myself one of these days:
1. The Hotel del Coronado. The Hotel Del (as it's known) is one of the most famous hotels in the country. Originally constructed in 1883 and built completely of wood, the Hotel Del simply reeks of charm and atmosphere and also sits on one of the most beautiful beaches in the United States (including Hawaii!). If you were a honeymooning couple or an older couple without kids, it is the one I'd recommend for you. But you're not, so I'm not recommending the Hotel Del. It is not convenient to the attractions you want to visit, it is *very* expensive, it is old enough that the rooms are relatively small by today's standards, and it holds little attraction for small children.
2. Paradise Point Resort. If I had small children, this is the place I'd want to stay in San Diego - hands down. When you come to Paradise Point you will literally think you've arrived in Tahiti. It is the only hotel in San Diego with a truly South Seas atmosphere. It is extremely quiet and secluded, yet it is the closest place you can possibly stay to Sea World - there isn't even a Motel 6 that is closer. It is built on Mission Bay and even with a 4 year old and a one year old, you'll come home from your vacation relaxed, refreshed, and with memories of fun-filled days and romantic evenings. There is easy access to Interstates 5 and 8, Mission Beach, Ocean Beach and Belmont Park are two miles away, the Zoo and downtown with its wealth of attractions are 5 miles away, La Jolla is six miles away and Legoland is 25 miles straight north off of Interstate 5. But the main thing is that once you're at the resort you'll think you're on a secluded tropical island, yet you'll have all the attractions of San Diego close at hand. It's definitely a step up from a Residence Inn - not cheap, but definitely worth the price for an experience you will always remember. In terms of a real vacation in the truest sense of the word, you could not possibly do better than Paradise Point Resort.
A good site for things to do in San Diego and San Diego hotels is:
http://www.san-diego-vacation-attractions-tours.us/
A few additional San Diego related websites are:
http://www.brokerforyou.com
http://www.medical-research-study-directory.info/san-diego-medical-research-study.htm
http://www.san-diego-plastic-surgery-cosmetic-surgery-doctors.us/
http://www.lasik-surgery-san-diego.info
http://www.sandiegolawyerforyou.com/
http://www.san-diego-dentist.us/
http://www.downtown-san-diego-real-estate.com/
http://www.san-diego-for-sale-by-owner.com/
http://www.la-jolla-ca-del-mar-san-diego-real-estate-encinitas-california.us/