Teddy Pasternak at 2011-08-19 15:48:32:
Since the two "entities are completely disconnected" you're going to have tremendous problems marrying them. That disconnect will eventually trickle down to an audience who will wonder why they're not connecting with the story.
My suggestion would be to create two separate stories. Take your protagonist with the unique flaw and plot a story for him - a story that grows out of that character. And use Scott's great suggestions. Ask yourself those questions.
Then, use your original plot with the twist and come up with a new protagonist that would fit better. Someone who the audience would benefit the most from watching. Someone who has to struggle and overcome the most obstacles on the way. Someone who has to travel the furthest to get to the end.
Here's your chance to tailor-make a new character to fit the plot. Could be an interesting exercise.