This movie....eh. Should be taken with a grain of salt..
Part One: Interesting stuff about religious/mythic connections. But I knew that already from reading Joseph Campbell. It doesn't mean there was a grand evil conspiracy, it just means that there are archetypal themes that resonate in humanity. Secondly,assuming there was no literal Jesus that walked the earth is silly. Just because he (IMO) didn't have magical powers that doesn't mean he was completely made up either. The Jesus Seminar was a group of scholars who tried to sort out what was historically likely from the source material (both canonical and non-canonical sources). They concluded:
The seminar's reconstruction of Jesus portrays him as an itinerant Hellenistic Jewish sage who did not die as a substitute for sinners nor rise from the dead, but preached a "social gospel" in startling parables and aphorisms. An iconoclast, Jesus broke with established Jewish theological dogmas and social conventions both in his teachings and behaviors, often by turning common-sense ideas upside down, confounding the expectations of his audience: He preached of "Heaven's imperial rule" (traditionally translated as "Kingdom of God" as being already present but unseen; he depicts God as a loving father; he fraternizes with outsiders and criticizes insiders.
Part Two: It was interesting to see the discrepancies. It doesn't prove a single theory, yet it should be looked into further.
Part Three: Again some interesting stuff. Again, it doesn't prove a grand unified conspiracy. And somethings are just flat out wrong, like saying that FDR was involved in letting Japan bomb Pearl Harbor. Completely untrue! Again, bits and pieces of historical oddities does not a grand unified conspiracy make.