Board Thread:Questions and Answers/@comment-67.1.246.12-20130810173702/@comment-4913740-20130902025718

Raiden as Eli is another theory that has been posed before, but it all depends on whether where we see Eli is somewhere in the Middle East or somewhere in Liberia. I'm leaning more towards the Middle East, and a lot more towards it being Liquid.

But Kojima is fond of retconning where he sees fit, so it could be anyone of the Snakes or Raiden at this point. It's just a matter of time before we know the full story.