We need to get a picture of Nadeshiko when she was little (in the episode where Sakura visits her great grandpa, I think, and compare it to the 10 year old Sakura).
I don't think she looks like her father. What she has from him, is his hair and color of skin, instead of her mother's fair (which is why people probably take the dad/daughter resemblance in). The rest, including the eyes and facial features, is/could be like Nadeshiko, which is why there is always the comparison between the two. It is mentioned for a reason, and if mostly everyone in the CCS world mentions it, then it must be true. Is proper for a girl to take after her late mother. Remember that they are both referred to as cute also.
As for Kobato, to make it short, she's Sakura with long hair, kind of long hair....