I work at the airport and Southwest is pretty much all of terminal one. I would allow 3-4 hours for a Southwest flight departure. And plan on luggage taking 45 minutes to arrive on the carousel when you arrive. For the other airlines, 2 hours is plenty of time to clear security, especially if you have TSA precheck. Sometimes, precheck is not open in terminal one, so that creates even longer lines. There are times when the TSA line goes beyond the normal "line area" and extends through baggage claim then loops back around almost to the checkin counter. There have been a few times where agents are often on bullhorns looking for passengers by name and expediting them through security...and other times there are people freaking out about missing their flights. It is especially bad on Fridays and Sundays and if a cruise ship is in port...forget it. Add two cruise ships and good luck. I refuse to fly Southwest because it is always a disaster there.
As far as getting to the hotel from the airport, you can use a cab or uber. Our airport was the first airport to actually put in a ride share app lane/waiting area. Its super easy to meet an Uber at San Diego Airport. There is a brand new Springhill Suites right across the street from the cruise ship terminal.
Extraordinary Desserts is a safe walking distance from the hotel and its amazing. You are also within walking distance of Little Italy (Bencotto is great as is Filippis Pizza Grotto). For seafood, try Anthony's Fish Grotto on the water. Next door to the cruise ship terminal is the USS Midway Museum and is definitely a great museum.