The T-rex loose in San Diego is a homage to both King Kong and Godzilla. The ship's name is a reference to King Kong and the shot where we see Japanese business men running along shouting "I left Japan for this" is a reference to Godzilla.
With the success of the first movie there was always going to be a sequel and Spielberg knew that people wanted to see one of the dinosaurs loose on the mainland. The Tyrannosaurus was the perfect choice. I personally love the ending and how it feels like King Kong or Godzilla but in the JP universe, its one of the best sequences in the entire trilogy.