Reddit mentions of Guide to Greece, Vol. 1: Central Greece

You mean like Zeus/Jupiter? The Romans took over the Greek pantheon more or less wholesale, and was generally enamored with Greek civilization throughout the rise and heyday of Roman civilization, so there's a large degree of continuity between the two. So there's a great deal in Ovid, and in Roman mythology as a whole, that more or less accurately reflects Greek mythology. And there were still Hellenistic Greeks around to connect the Roman versions back to something like the original versions. A particularly useful source is Pausanius' [Description of Greece].

Pausanias was a Greek traveller and geographer who served the Roman Emperors, in part by writing a huge digest of descriptions of Greek regions, cities and landmarks. And along with those descriptions, he recounted the legends and myths associated with the places, bequeathing to posterity a much fuller picture of the distinctively Greek milieu.

If you want to study up on the primary sources -- which is really the best way to start with nearly any historical study -- here's what I'd recommend. Start with the Homeric Hymns and Hesiod's Theogony -- the former is a solid introduction to the Greek pantheon and it's importance to the classical Greeks, and the latter will give you one (but, bear in mind, not the only) account of Greek mythological cosmogony and origins. Move on to Herodotus' Histories, which will give you not only a sense of the historical context, but also a great deal of myth and, paired up with a decent map of classical Greece, a sense of how all of this relates to regional differences. It can be useful to keep all of that straight since the Greek gods are, above all tutelary, and a great deal of the variations that you find in myths about particular gods can be explained as a matter of Theban v. Athenian v. Spartan versions, and so on. That he favors whatever version fits best into his unified narrative is one of the reasons that I hesitate to recommend Graves' The Greek Myths -- part of the pleasure of reading Greek myth is that its primary characters are so mercurial. Ovid's Metamorphosis follows Herodotus well, then Pausanias' Description of Greece, and at that point, you'll be nice and rounded when it comes to Greek myth. After that, you may want to go back and read the Greek tragedians, or brush up on the mysteries, or since actually reading all of that will probably take you years, you may want to never read about the Greeks again. That certainly hasn't been the case with me, but I can certainly see how some people might feel that they've exhausted their interest in the subject after that.

Getting back to the question you actually asked, I don't know of any books that focus on examining the difference between the Greek and Roman versions of the same myths. It would be interesting to read if there were one. I would be surprised if, even covering the same basic stories, there were significant thematic differences. Despite its investment in Greek culture, Rome was a very different society with its own cultural leanings, and it seems like it would be natural for them to handle Greek mythology in a slightly canted way. What I can say with some assurance is this -- Roman religion went well beyond the Greek myths and pantheon, introducing and syncretizing Roman tribal gods and eventually developing the Imperial cult. The Greek influence is really, ultimately a point of departure for understanding Roman religion.