Without Bryce’s intervention, Sarah might have met Chuck during the Omaha operation. She meets Bryce instead, and they have their romance. But Bryce then sends the Intersect to Chuck in a chain of events that ends up putting Chuck and Sarah together anyway.
In the movie Casablanca, when Rick says to his former lover Ilsa: “We’ll always have Paris,” he is referring to their brief romance on the eve of World War II. When he speaks those words to Ilsa in the movie’s final scene, Rick has accepted that he and Ilsa will never be reunited.
Similarly, when Bryce says to his former lover Sarah, “We’ll always have Omaha,” he is referring to their (brief?) romance on the eve of the Intersect war with Fulcrum. When he speaks those words to Sarah at the end of 1.10 Nemesis, Bryce is giving her a code phrase to reunite with him, but he’ll have to accept instead that he and Sarah will never be reunited.
And Sarah’s torn between two men at the end of Nemesis just as Ilsa is torn between two men at the end of Casablanca. But just like Rick for Ilsa, Bryce is for Sarah the ever-living ghost of what once was.