Stone Liberty Station is a cool spot to sit outside. I am a fan of Ocean Beach, a few breweries - Culture and Belching Beaver are good - and some good spots to eat. Hodad's has good burgers, South Beach Bar & Grill has pretty good fish tacos and Pizza Port usually has some good handles. North Park and Little Italy nearby also has some clusters of breweries. Farther north you have breweries in Miramar and Carlsbad. Fathom Bistro, Bait and Tackle is a cool spot on a pier on Shelter Island, they have a good tap selection.
If you get a chance, the beach towns in North County are cool, La Jolla, Solana Beach, Encinitas, Cardiff, Carlsbad. The Lost Abbey has a spot in Cardiff and Culture in Solana is pretty fun. Eat plenty of fish tacos. There are plenty of good breweries all over the area.
@SDV could offer suggestions as well. I do not spend time in downtown, my friends hate the Gaslamp district.