Well, you can read all 14 chapters if you want the complete context or just chapter 9. Below is the first paragraph of chapter 9. Darwin admits in his words "the extreme imperfection of the fossil record".
Chapter 9 On the Imperfection of the Geological Record.
IN the sixth chapter I enumerated the chief objections which might be justly urged against the views maintained in this volume. Most of them have now been discussed. One, namely the distinctness of specific forms, and their not being blended together by innumerable transitional links, is a very obvious difficulty. I assigned reasons why such links do not commonly occur at the present day, under the circumstances apparently most favourable for their presence, namely on an extensive and continuous area with graduated physical conditions. I endeavoured to show, that the life of each species depends in a more important manner on the presence of other already defined organic forms, than on climate; and, therefore, that the really governing conditions of life do not graduate away quite insensibly like heat or moisture. I endeavoured, also, to show that intermediate varieties, from existing in lesser numbers than the forms which they connect, will generally be beaten out and exterminated during the course of further modification and improvement. The main cause, however, of innumerable intermediate links not now occurring everywhere throughout nature depends on the very process of natural selection, through which new varieties continually take the places of and exterminate their parent-forms. But just in proportion as this process of extermination has acted on an enormous scale, so must the number of intermediate varieties, which have formerly existed on the earth, be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.
You're correct, Darwin gives many rationales as to why the record is so poor. As one would expect from the proponent of a theory.
But 150 years later the record is still, shall we say "less than perfect". And when you couple that with the discovery of DNA by Crick and Watson 50 years ago and the realization that the cell is not simply a sack of protoplasm (as was thought in Darwin's day) but a micro factory teeming with information and activity, questions and doubts will and are being raised about the validity of Darwin's claims.
Darwin's theory has had a good run. About 150 years. He deserves all the accolades he gets and will long be remembered as one of the greatest scientists of all time.
However it's time for science to move on. And we are witnessing a great scientific revolution it in our life time. Amazing. The history of science is one of revolution and change. Theories get created, destroyed, modified and tweaked. That's the history of science.
A good read on this process is "The Structure of Scientific Revolutions" by Thomas S. Kuhn 1962.