Loved the ending, was scared the other one would win though.
I mean ugly loner girl who's really a beautiful girl seemed like such a cliche choice that I was sure it was going to happen, despite Nishino developing better in every way.
During meiosis there's chromosomal recombination. Therefore the offspring won't be a clone since each gamete contains a haploid set of chromosomes that resulted from the recombination of the organism's two original chromosome sets.
Note that, according to the following study, each human genome has around 800 deleterious mutations. If an individual interbred with someone who was genetically almost identical (if we remove the Y chromosome we are talking about 98% sequence identity between the two genomes), around a fourth of these mutations would end up being homozygous. Things don't look so good for the resulting fetus.