The discourse about Sophie Baek being a perfect Mary Sue who's totally devoid of any flaws baffles me! She's secretive to the point of deceit, she's so anxious and insecure that she'll remain in a crappy situation for years rather than take the risk of improving it, she's a self-confessed observer rather than a proactive doer who allows herself to experience things (that's why her one night at the ball was considered such a radical departure from her norm!), she has rigid standards for herself and others and then sometimes melts down when they're inevitably not met, she's a worry-prone, serious and VERY guarded person who makes it hard to truly get to know her...etc. (I know most of this applies to the show version - if you want to argue that the book version is too perfect, I'd be more inclined to agree!) Yes, she's pretty, smart, kind, considerate and ultimately resilient, but she's FAR from perfect, and that's why I love her.
I really love that a major part of their story revolves around Benedict moving on from the seemingly perfect, peppy dream girl (aka The Lady in Silver) of his fantasies to the more serious, anxious, secretive, guarded and complicated Sophie whom he falls in love with in reality. The fact that Sophie WAS The Lady in Silver is just more amusing because only Benedict could get entangled in a love triangle with two entities who turn out to be the same person (it still makes me laugh!) but also interesting because it proved to Sophie that she CAN be someone who allows herself to experience joy and take risks and proactively change her life, none of which she had been doing.
As others have commented on, it's the fact that Benedict and Sophie both have clear shortcomings each can complement which makes them such a perfectly suited couple. Sophie brings Benedict back down to earth, inspiring him to act like a far more prudent, more selfless and thoughtful human being while he takes her out of her head and urges her to let herself feel real joy and embrace all that life has to offer.
