RESPONSE: To be honest, I do not invest much into these sorts of theories. Don't misunderstand me. I think they are fascinating, but I have no reason to find them compelling. I should say, right off the bat, that I do not consider the existence of extraterrestrial life impossible. I think it may even be likely given the size of our universe. However, there is a huge difference between life and intelligent life. And on a Christian worldview, there is an even greater difference between intelligent life and human life. There are some creatures that live in the darkest depths of the ocean that I am more than happy to call "alien" (although technically from this planet). It wouldn't cause me to question Christianity and the Bible if we eventually discover creatures like these somewhere in the farthest reaches of space. It would take a very specific sort of extraterrestrial life (conscious, moral, reasoning) to really do much to undermine the Christian view. I understand that is precisely what the ancient alien/astronaut theories suggest, but that is where I just don't feel like there is any compelling evidence. Anyway, that probably wasn't what you were asking, so I will move onto the Genesis 6 question since I have a good bit to say about that.
Genesis 6 is a chapter that fascinates and confuses a lot of people. Who/what were "the Sons of God" who fancied the "daughters of men?" Who/what were "the Nephilim?" I think it is unfortunate that so much confusion has arisen out of these couple of verses. Let me briefly explain why. The passage seems to indicate that what "the Sons of God" were doing was not something God approved of. First of all because the context seems to be all about the sinful spiral of humanity leading up to the flood. Beyond that, if we suppose that the Sons of God are angelic beings (as many do), then there is no reason to think that it was God's intention for them to breed with human women. Thus, in Gen 6 we are either dealing with disobedient humans or disobedient angelic beings. Up to that point, there should be no real disagreement.
Now, just so we are on the same page, disobedient angelic beings are also traditionally called demons. Angels and demons are by nature spiritual beings. That much is obvious in Scripture. However, it gets a bit tricky since there are instances in the Bible where angels take on physical form (at the very least making them visible to the human eye). This is called an "angelophany." But the important question here is: from where does this ability to take on physical form come, and what purpose does it serve? In all of these cases, the angels are serving God's purpose and it is he who gives them physical form. He is the creator of all things physical and immaterial. Thus, there is no room for rogue angels going around and manifesting bodies in order to satisfy their lusts. That is something out of ancient pagan mythology. Unfortunately, many people (even many good theologians) have spliced it into their understanding of this text. If there is any hybrid, mutant, creature being created here, it is only the result of bad interpretation.
Now, you may have never thought about it before, but if demons have the power to manifest human bodies, then that opens the door to a whole host of problems. First of all, how can we know that anyone we encounter is not a demon that has simply taken on flesh? My friends could be demons. And if we take the approach that many people do to interpreting Gen 6, one of my parents might be a demon (surely many children have thought this). What would that make me? Are there others like me? It sounds like a good concept for a graphic novel, but it is not biblical. Much more important is this: how can we know that Jesus actually rose from the dead? What if what the disciples saw was just a demon? We know that the Pharisees accused Jesus of conjuring demons to do miraculous signs. Is there any evidence that what the disciples saw wasn't a demon? Jesus provided a very powerful piece of evidence when he told his disciples that "a Spirit does not have flesh and bones, as you see that I have" (Lk 24:39 NASB). When they still weren't convinced, he picked up some food and ate it to demonstrate that he was a physical being. I hope you can see that if we grant demons the power to manifest physical bodies, then Jesus' line of reasoning becomes nonsense.
Alright. So I have explained why I don't think that demons took on flesh and procreated with human women in Gen 6. The last question then is: what on earth are these verses talking about? Briefly, it is my understanding that "the Sons of God" refers to the godly descendants of Seth, and "the daughters of men" refers to the corrupt descendants of Cain. As I said above, the context is all about the sinful spiral of humanity leading up to the flood. In sum, these verses tell us that those who followed God were enticed to marry and procreate with those who did not, and the result was a continued descent into depravity. That leads us to verse 5 (all of the talk about Sons of God and Nephilim is in verses 2-4) where we read, "Then the Lord saw that the wickedness of man was great on the earth, and that every intent of the thoughts of his heart was only evil continually" (Gen 6:5 NASB). In my mind, it makes perfect sense given the context and does not require any hermeneutical gymnastics. Nor does it require me to believe that demons have the power to take on flesh and procreate with human women, since that such an idea is totally at odds with the rest of the biblical record. This interpretation will undoubtedly seem boring and uninteresting to some, and I am sure that I will get plenty of pushback, but I hope it helps.
*UPDATE: In less than an hour after posting this, I have gotten several emails and messages through social media. Some of these have employed very heated language. Please understand that I consider the question of how one interprets Genesis 6 to be a secondary issue and admit that I could be wrong. However, inasmuch as I believe it has implications that are tied to the resurrection--particularly answering critics who would say that maybe a demonic spirit deceived the disciples--I take it very seriously. I would not consider this an issue worth dividing over with any fellow Christian. As long as they understand my concern to defend the resurrection of Christ and proper biblical interpretation we can agree to disagree and work out the question together.