Bioengineering
The Human Race was bio-engineered by an alien race. Several million years ago, before humans came on the scene, there were primates (monkeys, gorillas, chimps etc). A highly evolved species visited our planet and noticed striking similarities between themselves and the creatures roaming Earth (all alien sightings say that the aliens have 2 legs, 2 arms, 5 digits per limb, torso, head, 2 eyes, etc). Curious about their own evolution, they decided to artificially inseminate some of these creatures with their own sperm to find out how they might have developed (they may still do this today to insure quick evolution: many abduction survivors say they were made to have sexual intercourse with something). The result of this was a quantum leap from primate (presumably chimpanzee: 98% of our DNA is identical to theirs) to homo erectus, then to homo sapiens (modern human).
During the early days of man-kind, the aliens guided us (almost every religion has a "god" that actively helped man-kind: because of their vast technology, they would certainly be regarded as gods). The great flood of which only Noah and his family remained (every religion in the region mentions this) could be the aliens attempt to cull off all inferior genotypes to get the best results, like a gardener only plants seeds from strong plants.
The reason the aliens elude us is, as any scientist will tell you, to create a fair experiment, you must prevent any interference. So, while they still observe our process, they try to keep it low impact.