In the end we all know he's hesitating because he's judging between being true to himself, thus becoming a human wretch by loving his sister romantically and, on the other hand, accepting Kuroneko, whom he does like, maybe even love in some manner, but not with any romantic passion. In other words he's wondering whether to live like a human with some regrets (by accepting Kuroneko) or whether to live without regrets but also miserably doom himself (by choosing Kirino).
He would have been wise to check AniDB and see Kirino has a rating of 4.62, whereas Kuroneko has amazing 8.53 (the legendary Tohsaka Rin has 8.42, so you can see how highly rated Kuroneko is). After seeing that, it's not really anymore even a proper question.