I have read on occasion that they kept the pantheon out of admiration and/or to keep the peace with the newly conquered Greeks, but I have never seen any hard evidence or writings that say this in in fact true. Are there any historical records out there that confirm or deny this?
closed as off-topic by Dan the Man, Kobunite, Lennart Regebro, Steven Drennon♦ Sep 10 '13 at 23:39
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Humans are story tellers. We understand the world through stories, and spread the stories we like and make sense to us. As such, religion tends to be about stories. We have creation stories, thunder gods, gods intriguing amongst themselves, falling in love with humans, testing human devotion, etc. All stories designed to help humans to build a picture of reality that it can understand and accept.
Obviously then, the best of these stories will spread around, and be picked up no matter where they originally come from. As such there are stories in the Norse religion that clearly comes from the Greek mythology, and of course the famous flood story in the bible comes from older Sumerian flood myth. Polytheistic pantheons are also by nature somewhat similar. You'll have some sort of thunder god, a fertility goddess etc.
Contacts between Rome and Greece goes back to further than the roman empire, and before any historical sources of Roman mythology, and as such many of the stories would be the same already when the Roman empire started to spread. A good foreign story about Zeus the thunder god would be applied to local thunder gods. Romes admiration of Greek culture in general also meant that they were even more prone to add the Greek stories to their own gods, and after a while the difference was hardly discernible. Polytheistic religions also have no problems in adding new gods to their pantheon unless they conflict with existing gods.
This can make the list of existing gods rather huge, and as nobody can remember the minor differences between 20 thunder gods when you have several hundred gods to keep track of, you quickly start merging similar gods together. This can be traced back as far as 2nd or even 3rd millennia BC. An additional reason to identify two gods is that is increases the apparent reach and power of these gods by putting them not in conflict, but just two aspects or names of the same god.
In both Hinduism and ultimately also in Mesopotamian religion, this process in fact ended up with the declaration that all gods are ultimately only aspects and incarnations of the one god (Vishna or Krishna in Hindiusm and Ashur in Assyrian religion).
Although this process can more easily happen in polytheism as areas with polytheism more often will accept religious freedom, it can happen with monotheistic religions as well. Examples of this is the acceptance of Jesus into Islam, although he gets to be "demoted" to a prophet, to the multitude of universalist religions in existence today.
So in short, the answer to why the Romans incorporated the Greek pantheon into their own is rather "Why not?" It's a more difficult question to look at places where his did not happen and explain that.