She wishes that she was half as good of a person as Stefan believes her to be.
Though he swears that it is Damon who is incapable of seeing shades of gray, Elena knows that the world has been cleanly divided in Stefan's mind into "right" and "wrong." In the beginning, it was her favorite thing about him. After Wickery Bridge, she had needed the absolutism that he had offered.
But that was before Katherine and Elijah and Klaus and a thousand other things that have made her moral compass start to spin a little more south.
Stefan wants to save her, mend the damage that Katherine has done to her world, and she loves him for that. She adores the fact that he wants to give her as much normalcy as possible, knows that he would move heaven and earth to keep her happy, but she is starting to realize that the girl he fell in love with is not the girl she is now.
She realizes it when he is upstairs with Katherine, doing whatever needs to be done with Jonas. Damon is echoing her thoughts and beliefs on Katherine, standing a little too close as is his way, and she is suddenly hit with the realization that she has agreed more with Damon in the past few weeks than she has with Stefan.
There was a time when it would've horrified her, that the thought of being in sync with Damon Salvatore would have thrown her into full existential crisis.
Now, she leans into it, accepts it for what it is, and minutely moves closer to his body, thick with tension.
A few days later, after Isobel has left, she is sitting on the couch in the boardinghouse while Stefan hunts. Damon comes downstairs, gravitating to the bar as always; he pours himself a tumbler of bourbon before asking, "You want?"
She nods, surprising both him and herself, and sighs as he sinks down beside her.
They are still sipping their bourbon in silence, fire dancing before them, when Stefan comes home.