He doesn't understand the meaning of Kensuke's unexpected words right there and then, but he somehow starts to feel happy, and, smiling, takes a step forwards!
KENSUKE (OFF):“That means the two of you are family...”
UrsusArctos: "Such a cool ending"...if only more episodes ended as happily as this!
This is a metaphor for the distance between Shinji and Misato growing smaller!