Because the organs and systems ARE homologous, it points back to a common ancestor. It means sexual reproduction didn't have to arise several times, only once. All sexually reproducing organisms derive from a common ancestor which could have been a single celled eukaryotic species. Many protists reproduce sexually, as do the multicellular plants, animals, and fungi. There are a few species which have secondarily lost this feature, such as Bdelloidea and some parthenocarpic plants.
Organisms need to replicate their genetic material in an efficient and reliable manner. The necessity to repair genetic damage is one of the leading theories explaining the origin of sexual reproduction. Diploid individuals can repair a mutated section of its DNA via homologous recombination, since there are two copies of the gene in the cell and one copy is presumed to be undamaged. A mutation in an haploid individual, on the other hand, is more likely to become resident, as the DNA repair machinery has no way of knowing what the original undamaged sequence was. The most primitive form of sex may have been one organism with damaged DNA replicating an undamaged strand from a similar organism in order to repair itself.
Another theory is that sexual reproduction originated from selfish parasitic genetic elements that exchange genetic material (that is: copies of their own genome) for their transmission and propagation. In some organisms, sexual reproduction has been shown to enhance the spread of parasitic genetic elements (e.g.: yeast, filamentous fungi). Bacterial conjugation, a form of genetic exchange that some sources describe as sex, is not a form of reproduction, but rather an example of horizontal gene transfer. However, it does support the selfish genetic element theory, as it is propagated through such a "selfish gene", the F-plasmid. Similarly, it has been proposed that sexual reproduction evolved from ancient haloarchaea through a combination of jumping genes, and swapping plasmids.
Sex may also be derived from prokaryotic processes. A comprehensive 'origin of sex as vaccination' theory proposes that eukaryan sex-as-syngamy (fusion sex) arose from prokaryan unilateral sex-as-infection when infected hosts began swapping nuclearised genomes containing coevolved, vertically transmitted symbionts that provided protection against horizontal superinfection by more virulent symbionts. Sex-as-meiosis (fission sex) then evolved as a host strategy to uncouple (and thereby emasculate) the acquired symbiont genomes.
But just because we don't know the exact answer yet, doesn't mean an answer won't be found. And no matter how many particular holes who think you see, it won't prove your particular God, and it isn't even very good POSITIVE evidence for an Intelligent Designer to be named later.