Here Darwin addresses concerns/confusion concerning his theory of natural selection. In this chapter, Darwin addresses a lack of transitional forms and the so called perfectness of specific structures.
Transitional forms: Darwin recognizes that transitional forms are replaced by successive generations of forms, but questions why there is a lack of fossil evidence (1). There were known fossils in Darwin's time, but not to the extent that there are today. Fossilization is a rare process, and most individuals are destroyed. For instance, there is very little information on chimp evolution due to the fact that so few fossils from that lineage have preserved.
For instance Archaeoptreryx lithographica, an early feathered dinosaur, was not discovered till 1861. Since then, only 7 specimens have been found (2). However, obviously for the species to exist, there had to be much more than 7 individuals.
To address the question of why we don't see transitioning forms today, it's because we don't know what they're transitioning into. Evolution is a very long, slow process.
Darwin inferred from the geological record that Earth in modern times is experiencing a more stable array of climates (of course this is pre-global warming concerns). Therefore, in times of great climate shifts and unstable environments, life may have had to adapt more extremely. Darwin asserts that "continuous conditions" are mainly responsible for the diversity of species populating the world. This means that life is not restricted to one zone, but differs in distribution for select climates (1).
However, it's not just about climate, it's about other species too. The predators, the prey, the whole circle of life bit. Speaking of which, The Lion King (the first movie I ever saw in theaters!) demonstrates a lot of Darwin's ideas. Work with me here, the hyenas move into the lions territory and eat up all the food subjecting the lions to the choice of either finding a new territory or starving to death. Of course in the movie there is option 3, kicking the hyenas out of pride rock in a symbol heavy disney ending, but that's adaption! As a side note, the lioness' fitness was really suffering through that movie. There were only two cubs and then no males for a very long time.
Okay, enough pop culture, back to the book. Darwin brings up the genus Balanus, and that individuals appear as intermediates between the main varieties (1). What exactly is the genus Balanus? Well, it's a type of barnacle. Darwin was a bit of an expert on barnacles so I'm going to trust him on this. He has a multi-volume book about barnacles (he might love them just as much as pigeons, though I don't think that a barnacle can express as much response as a pigeon -- I imagine them to be along the lines of pet rocks, but perhaps less exciting) which I will not be reading.
Darwin also addresses species that are highly adapted to specific behaviors. His choice example is the bat evolving from a flying squirrel, and a whale evolving from a bear (1). These are very theoretical and very wrong; while bat evolution isn't well documented, whale evolution is and they evolved from large land carnivores (that weren't bears).
Next, Darwin covers so called perfect structures, namely, the eye. We now can trace the mosaic evolution of the eye, but such advances weren't available to Darwin who seems baffled by the perfection. However, he was very certain that all features in species can be explained by gradual change. One argument he uses is that certain organs or features may end up being used, and adapted, for a completely different use than how they were originally selected for (1).
Darwin goes on to discuss vestigial organs (without directly calling them that). He muses that they are leftovers that were useful to an ancestral form, which is true. His other concern is of traits that are assigned importance, but are just by-products of selection. Also, Darwin finally brings up humans, specifically races but doesn't have any explanations for them (1). Which is probably for the best.
1. Darwin. On the Origin of Species, 2nd ed. 1861.
2. Archaeopteryx lithographica. Dinosaur World. 2007. http://www.dinosaur-world.com/feathered_dinosaurs/archaeopteryx_lithographica.htm