many people believe ET is supposed to be a Christ like figure and symbolizes when Jesus Christ was crucified, eventually resurrected and was taken into heaven (ET was taken home by a UFO at the end of the film) when ET tells Eliot he will always be "right here", and gestures to Eliot's heart, is believed to symbolize the Christian faith.
Personally, I believe it's a story of how friends come from all sorts of places and may look different but give a genuine friendship. Kind of a "don't judge a book by it's cover" story.