It creeps me out too, whenever I see a “faceless face” like that. Probably the only part of Nayuki’s route that I didn’t like. Though I guess you could always draw your own face over it…
Regarding cousin-based relationships, it didn’t bother me. The wikipedia article @HeliosAlpha posted even mentions that the only biological ramifications are nearly the same as elder women giving birth. With the biological issue neutralized for the first cycle of first-cousin relationships, there’s no argument left against it that can be explained in a purely logical way. (Unless I’m just not seeing it.)
BONUS TIME! Fun phrases I’ve heard (don’t do this at home): “If you can’t keep it in your pants, keep it in the family.” “Incest-is best-est.” That’s all. Excuse the terrible jokes.
Nayuki’s route, and maybe this is just me, was fantastic. Nayuki grew to love Yuichi all these years. (Kanon) Even when he didn’t tell her about Ayu. Even when he was taking care of that fox without her knowledge. Even when he broke her snow bunny. (Note to self: Make a snow bunny someday. It’s okay Nayuki! I’ll make you a new one!) He was never really there for her, yet she somehow came to love him. At least, “seven years ago.” Now Yuichi comes back, and he doesn’t remember anything from back then? Just fragments and pieces? Nayuki uses her strength to keep smiling. Only after Akiko’s accident does she lose that. (And, damn, her reaction isn’t all that bad. Especially considering it wouldn’t have happened had Akiko not went to get her the cake.) So how does Yuichi try to fix the situation? He searches. He tries to think of a way to help her. After having been unreliable in the past, he decides to fix the past to show that he can be reliable. So he goes back to the spot outside of the station, to meet her again. To show that he’s willing to wait, just as she was. To show that he can be there for her, with actions, not just words.
I was planning to say more or elaborate further, but that’ll have to wait for another time… (Perhaps on Nayuki day December 23rd.)