As much as I hate the S3 relationships, I do see a purpose for them within the internal logic and structure of the show. This is a show built on counterpoint and patterns. Both Chuck and Sarah face the ghost from their past (Bryce, Jill). Both face the temptation from their present (Lou, Cole). Both need to be free to face the reality of a future with that temptation (Hannah, Shaw) to realize it’s only half of their real life—Chuck and Hannah share a normal life but no spy life. Shaw and Sarah share the spy life but no normal life. Only together can Chuck and Sarah have both, a full double life.
And this realization is bookended by Devon and Ellie, who symbolize the ideal couple in Chuck and Sarah’s life. Devon is the one who warns Chuck at the end of 3.03 Angel de la Muerte about the perils of living only half of a real life, and Ellie is the one who inspires Chuck at the end of 3.10 Tic Tac to rethink Prague and pursue Sarah again, and she is also the one who inspires Chuck in 3.12 American Hero to finally reverse Prague and put Sarah first.
And after he does that, both Chuck and Sarah joyfully realize at the end of 3.14 Honeymooners that they can have their full double life—a real life and the spy life, love and duty. They can have it all.