Hannah is made to be the well-adjusted female version of season-1 Chuck—funny, charming, nerdy, sweet, innocent, open-hearted, loving, trusting, bright, looking for a real relationship. All the positives that Chuck had in season 1 but without the negatives (neuroses, self mistrust, and self loathing). So, in a sense, yes, she is perfect for Chuck because she is Chuck, a well-adjusted female Chuck. Down to her job as a grossly overqualified nerd herder who lost a bright future in technology, just like season-1 Chuck. Her chuckness is the reason Morgan immediately falls in love with her.
In season 3, Devon, Manoosh, and Hannah are all partial representations of season-1 Chuck—Devon is Chuck the unintentional spy, Manoosh is Chuck the mark/asset, and Hannah is the vulnerable, innocent, and charming nerd herder in want of a real relationship and who falls hard for a spy.
The way Chuck handles Hannah is hurtful because, during his douche spy phase (3.05 Chuck Versus First Class to 3.08 Chuck Versus the Fake Name), he treats her in a way that Sarah was unable to with season-1 Chuck, and he does so to the best version of himself in the form of Hannah. Being honest with Hannah (himself) at the end of 3.08 Chuck Versus the Fake Name is the first step on his path to redemption (3.09 Chuck Versus the Beard to 3.12 Chuck Versus the American Hero).
But in truth, Chuck and Sarah are perfect for each other because they are different; they don’t just mirror each other, like Chuck and Hannah, but complete each other. Sarah models competence for Chuck and encourages him from the very beginning to overcome his self mistrust and to see himself as the hero he is. And Chuck models innocence and vulnerability for Sarah, awakens her sense of reality versus appearance, challenges her moral imagination, and inspires her to turn from “nothing but a spy” into a woman who allows herself to love and be loved.