The Problem of the Omnipotent Villain, the Do's and Don'ts.

I have decided to specifically talk about movies in this post.  Books will be done at an unspecified later date.
In many pieces today, the author will find it prudent to use a near omnipotent or actually omnipotent figure as the villain.  There is logic behind it, as with a godly villain the hero will always be the underdog and always be more sympathetic to the audience.  Of course, the main goal in doing this is to allow for the bypassing of character development.  If we know he's good, has a tough road ahead of him, and has some human problems, making him have a decent personality isn't really necessary. 
However, the gigantic flaw that every movie with an omnipotent villain has is: how does the hero finally defeat the villain?  Most of the time, it involves three things.  Three extremely improbable occurrences.
Firstly, the villain will not kill the hero during their first encounter, despite killing many of the hero's comrades.  This is either due to arrogance or the hero's good luck, but either way it is laughably unlikely.  Take, for instance, Clash of the Titans.  The main villain, Hades first meets Perseus when he transforms into a fireball and blows up the ship Perseus was on.  Perseus's incredible lungs save him from drowning.
The second time they meet, Hades kills several soldiers who are standing next to Perseus.   So, despite having ample opportunity to end Perseus's life not once, but twice, Hades instead chooses to go hire some henchmen to do the job for him...  brilliant.
Secondly, there just happens to be a weapon that can stop said Omnipotent being.  Whether its a magical sword or nectar of life, or in the case of Clash of the Titans, a monster's head.  Undoubtedly, this item will be stored in a far off land, and require a perilous quest in which many of the hero's friends will die.  Of course, the villain will have ample time to kill the hero during said quest, but will not take advantage of the opportunity himself, instead sending various henchmen instead.
Lastly, there is a final confrontation.  In this the villain will have an overwhelming advantage, but rather than, say, immediately kill the hero he will allow the confrontation to drag on until the hero finally figures out a way to win the battle.
This happens in every single movie.
And it makes no sense.  Every time, the audience is left wondering "why did he not kill the hero way earlier?"
The thing is, omnipotence can be done right, just look at the Cthulhuverse by Lovecraft, as a primary example of fantastically done gods.
So why aren't movie producers willing to make intelligent plots with believable gods that actually act like gods instead of clowns?  You tell me.