As an Atheist...

Let me begin with this: All this started while I was listening to the story of birth of Lord Ganesha. (FYI it is customary to listen to the story on the eve of Ganesh Chathurthi.). Interestingly there are some weird references and connections between Christian, Hindu, Roman Mythologies and some science fiction/fantasy myths such as the philosopher’s stone.

My theory is that all the so called gods are mutants- Mutants as in science fiction: Humans with super human capabilities. This statement especially holds true for hindu gods, for it is said there are three crore (thirty million) gods and goddesses out there.

Rain god Varuna for instance, possesses the same powers as the Storm holds in X-men.

Lord Shiva’s third eye is mentioned to be capable of burning everything in its sight. This is reminds of Cyclops in X-men, except that he doesn’t have a separate eye to burn things. (For Naruto fans out there, Amaterasu is something similar, isn’t it?)

The “Samanthaka Mani” has the ability to give its possessor a mass of nearly 16 kgs in gold every day (as mentioned- 8 manugulu). It is an obvious reference to the Philosopher’s stone.

Cupid is the Roman version of the Indian Manmadha. Manmadha’s wife is Rathi, who is the goddess of sex.

Athena – The goddess of knowledge and wisdom refers to the Goddess Saraswathi.

Moses/Jesus shows his power of telekinesis when he parted the Jordan river to pave way for his followers. This is demonstrated by the powers of Jean Grey in X-men.

Sai Baba is said to have transmuted water into oil, when his devotees couldn’t buy oil to light lamps. Also, he’s said to have dispensed ‘holy’ water from his toes.

Hanuman is the Hindu equivalent of ‘Superman’. He has super human strength and he could fly too.

Vali and Sugreeva brothers are ape-men who could communicate with both humans monkeys alike.

The God’s omniscience could be an amplified version of Charles Xavier’s power to read, write and modify one’s thoughts. (Yes, that’s a pun on computers)

The King of Heaven Zeus is analogous to Lord Indra who is the king of Heaven according to Hindu mythology. Also there is a striking similarity between the weapons wielded by both. Zeus’ weapon was the Lightning and Indra’s weapon was Vajrayudha which by my understanding commands lightning. (Referring to the lightning rain Indra caused on Gokulam when people started worshiping Mt.Govardhana instead of Indra, himself.)

All this references I found only by the limited knowledge I have on each of the mythologies and I wish I knew more so I could find some more.
The reason the so called son of god/prophet is born once in thousands of years is that he is a mutant in real life. Out of all the possible combination of genes, there is still a definite non-zero chance that such a mutant will be born some day and that wouldn't come often. Even the Hindu mythology says that the god shall take a human form to help mankind once every yuga (it is a period of several thousand years). It's nearly the same as the odds of super human taking birth on the planet earth.