There's a neat article from a few weeks back about polytheism posted at “The Tao of D&D”. It's a bit long, but a lot interesting, so worth your time.
One of the philosophies espoused in the article is that the gods should be great and powerful beings who "can smash a PC, or kingdom like a bug", far beyond the “glorified monsters” they appear as in Deities & Demigods. So where did Messrs. Ward and Kuntz come up with the idea of the gods as creatures who should have stats and could be defeated in combat?
Probably from the myths themselves.
These myths are hardly consistent when it comes to the powers of the gods. Isis could flood the Nile with a single teardrop, but had to spend time disguised as a common, mortal nursemaid in order to rescue the body of the murdered Osiris. Yep, murdered, as in slain, as in reduced to 0 hit points (or -11, depending on your house rules). Osiris was lucky; he got resurrected. Poor Baldur wasn't so fortunate and ended up staying dead.
And Baldur was hardly unique among the gods and their brethren. Zeus slew his father and imprisoned the other titans. Tiamat was dismembered after her husband was killed (arguably in self-defense) by their children. Heck, the entire Norse pantheon was doomed to die in battle against monsters and frost giants.
Dying and torment were not unknown to the gods. Nor were they omniscient. Odin lost an eye and hung for three days from Yggdrasil, the World Ash, to earn the right to drink from the Pool of Wisdom and learn the making of runes. Thor was fooled by illusions. Ares was driven, screaming in pain and horror, from the plain before Troy by Diomedes.
Having said all that, I think most folks will get more mileage from the system outlined in “The Tao of D&D” because it tends to agree with people's default assumptions. We tend to think of gods as mystical forces rather than flesh-and-blood creatures, and we assume the relationships our characters will have with the gods will be distant, obscure, and personal, rather than matters of civic duty, akin to jury duty and paying taxes. If you're going to do something other than that with your deities, you should probably make them central to the campaign and its themes, as was done in the Dragonlance campaign.
Art Credits: Frederick Arthur Bridgman, Bertel Thorvaldsen.