My opinion is that man is the only intelligent life in the universe and that UFOs are simply physical phenomena - or perhaps spiritual ones which we do not yet understand. But they are within the sphere of our shared and conventional human lives and experience. That is why these stories are prevalent in our literature.
However, if it is true, the existence of aliens more advanced and older than human beings on Earth calls into question everything that we have been taught about orthodox Christianity for the past 2,000 years. (There were disagreements that were resolved by Church Councils which are resolved by Church Councils that resulted in this orthodoxy.)
For example:
The creation story. Orthodox Christianity teaches us that God created the earth even though Genesis refers to the firmament and to heaven which could be the entire universe. It further teaches that Adam and Eve were the first two humans from whom we all are descendants. It also says we were made in the "image and likeness" of God. So if there are aliens who resemble insects, or perhaps something we have never seen before, of what were they made in the image and likeness? Or, perhaps, were there multiple creations throughout the Universe? If so, are there multiple Genesis stories?
Jesus Christ. Orthodox Christianity teaches us that Jesus was not just the "son of God" but that he is himself divine and eternal. He was born of a woman (Mary) but her conception was immaculate. That is, the result of a divine act of the creator of the universe. One might infer that Jesus was the result of genetic modification or some sort of cloning, but that is not what the Bible teaches us. Furthermore, how does that square with his death and resurrection and the atonement? Sacrifice and substitution are core teachings of the Bible.
The nature of God himself. Again, orthodox teaching is that we look like God. But the teaching is also that God is the creator and sustainer of all things. Historically, that has referred to us as HIS creation and a single creation not multiple creations. It would be easy to infer that that God created these other civilizations but what does that do to our understanding of our relationship to God on this planet? We would have to shift our understanding to share our relationship and our creation and place in the universe with other intelligent life on distant planets. The universe will no longer be humancentric or earthcentric.
Certainly, it would cause us to have to re-examine Biblical teaching and literature and perhaps our understanding of fundamental Christian tenets mainly in relation to the purpose of Jesus's death and resurrection. Perhaps it was not about restoring a broken relationship with God through resurrection and eternal life but rather about the evolution of man's consciousness.