We're nearing on the homestretch with chapter 13, there's only one chapter after this one and it's basically a summary of Darwin's theory.
So here we go: Darwin begins by analyzing the shortcomings of the classification system, while it can show relationships, they are not very informative when it comes to inheritance and descent. Darwin was especially concerned with similarity in body plans and symmetry, as well as non-specialized traits and their impact on showing classification groups. He was also a proponent of discovering the genealogy of closely allied species and using that to classify them. However, in Darwin's time, it was difficult to discern genealogy without the knowledge and technology of DNA analysis.
Darwin explores the concept of convergent evolution, in which different species come to have the same adaptation but not from common ancestry but rather similar modifications. Darwin does not call it convergent evolution, but the concept of bats and birds having wings for the same use and not because they share a recent ancestor was recognized at the time by Lamarck's classification system. One example he gives that whales and fish have similar exteriors because they're adapted to the same surroundings but they themselves are not closely related.
On morphology, Darwin asserts that crucial parts such as limbs are reworked from an original template rather than completely thrown out and grown anew (ie: the fin of a whale is a modified leg from a former terrestrial ancestor). Darwin saw the analogous body plans of many different species as proof of common ancestry rather than a creator.
Darwin also talks about embryology and the similarity of early embryos of related species as well as how embryos are adapted just as well as adult forms for the conditions surrounding them. Darwin uses the example of a pigeon, shocker, to measure differences in juvenile and adult pigeons of different breeds to show their similarities at the juvenile stages. Darwin went off popular theory that embryos resemble ancient species. While they are simple and basically laid out I don't know that I agree with that exact assessment.
Darwin also covers vestigial traits, which he refers to as rudimentary organs and cites instances of underdevelopment in some individuals and fully functioning individuals. Vestigial organs are somewhat controversial today, because for some examples it is possible that the function is currently unknown. However, in most cases it is found that vestigial organs were useful in an ancestor and have now been replaced or rendered useless but are retained.
And finally, I thought this quote was pretty funny out of context, "For the male is a mere sack, which lives fora short time and is destitute of mouth, stomach, or other organ of importance, except for reproduction," (Darwin 369). He was referring to male larvae becoming "complemental males".