The chief's secular humanism seems to win out over the priest's religious devotion, and the natives never seem to take the whole gods thing too seriously to seem backward. Tulio and Miguel's friendship is a strong theme, but so is unrepentant greed. Near end, they leave the city with a boatload of gold, only to lose it in a tidal wave. But El Dorado fails, again and again, to really capitalize on what's going on. Make the characters have real changes of heart by then end, and you'll have a much better movie.
Some scenes succeed brilliantly.
At one point a giant rock-jaguar is tearing through town and picks up a guard by the mouth. He ends up being thrown up and out, landing beneath it. But then it fails in other parts. One failure is the music. El Dorado 's sound track is filled with crap about the path we paved together, friendship, etc., etc., crap.