I'm most of the way through Dawkins' Greatest Show on Earth, and while I don't take issue with most of the content that's presented, the way in which it's presented is often disingenuous and misleading.
First Dawkins' opening chapter declares evolution as a fact. And to the extent that biological evolution factually occurs, that it has occured, evolution as process, is a fact. Dawkins goes on throughout the book to conflate (or intentionally obfuscate) the fact of evolution-as-process with the non-fact of the entire evolutionary paradigm. The key point where I diverge from the evolutionary paradigm is on common descent, and the evidence presented for it is paltry and utilizes complete non-sequiturs. The argument is made (inferentially) in this form:
1. Evolution occurs
2. We can trace the lineage of various animals to various common ancestors
3. We all share a single common ancestor
Clearly this conclusion does not necessarily follow from the premises, and is only arrived at via assumption of metaphysical naturalism. The actual evidence is at least as compatible (if not more compatible) with the creation paradigm. That is, multiple common ancestors are at least just as likely, if not more likely. In response to evidence for this (i.e. Cambrian explosion), he simply postulates that pre-Cambrian animals didn't yet have hard skeletons, thus didn't fossilize. Which is fine to postulate, but the sudden appearance of diverse life during the Cambrian features the instant (in terms of geological time) appearance of not only hard-skeleton creatures, but the instant indepedent appearances of them along different evolutionary lines, at vastly different sizes, with already-intact predation relationships etc. No possible widespread environmental or predation stress can explain the sudden appearance of such hard skeletons and such relationships in such a short period of time. Indeed, he doesn't even postulate a possible pressure that could have resulted in hard skeletons appearing everywhere at once (again 'at once' in geological time, over 10s of thousands of years, but relatively very short).
The remaining evidence for common descent is relegated to homology in genetics. And specifically homology extending beyond the apparent functional parts of the genome, to the apparently useless parts. The argument (again, inferentially) being 'why would a creator create junk DNA AND make that useless DNA similar in different species?' The same main argument that theistic evolutionists make. Homology in genetics itself is easily explained by a creator using a certain design template that is similar from species to species. And the similarity of junk DNA can be explained in that it's only seemingly junk, and indeed, the more we discover, the more apparent junk is revealed as functional. Not only in DNA itself, but also in our own morphological features. In humans the adenoids, tonsils, S-shaped backbone, appendix etc. were all once thought to be useless evolutionary byproduct, and have all since been revealed to have specific, necessary functions.
Now the vast majority of the book doesn't even purport to defend common descent, but merely 'evolution'. Thus I don't take issue with the vast majority of the book, more with what it doesn't contain, and what the evidence doesn't actually support.
I enjoyed the section on the Lenski team experiment, which is fascinating stuff. Dawkins' tone during that section is that of a giddy fanboy. Which is fine, I suppose passion about your field is a good thing. Though, again, the evidence as it relates to the evolutionary paradigm, only supports much of which we already knew to be true. And the new information that the experiment DOES provide strongly suggests that evolution occurs and is highly historically contingent, which is a problem for the evolutionary paradigm on the whole, not a support for it.
The following is more of a stylistic issue, but it's funny how Dawkins can not help himself. At the beginning of the book he says that the book isn't about God, religion, evolution-vs-religion etc., but simply the evidence for evolution. Then throughout the book he brings up creationists (almost exclusively young-Earth creationists specifically without ever making that distinction explicitly) often, and in so doing, never adds anything to his evidence for evolution. Seemingly just pandering to his anti-God audience, tossing red meat to his followers for no other reason than to sell books. Or possibly to keep lay people interested in the potentially complicated and/or dull material.
Another stylistic thing, but his conscious attempt to create memes is hilarious. He's just so bad at it. I believe in one of his earlier books he created the useless term 'quote-mining', which is just another name for taking a quote out of context, really. In this one he attempts to encapsulate anti-evolutionists in the most catchy, derisive way possible and this is the 6-syllable term he came up with: 'history-deniers'. LOL.