Fannie and Freddie: What Now?

Good question! Unfortunately, this article doesn't have any answers.
So I will offer one of my own. It is not really a solution to the problem. But it is something that may actually be more useful, since in today's world, no one with any sense is actually allowed to solve any problem. The Federal Government will continue with the Ponzi scheme these entities currently are until they cannot any longer. At that point, they will dump all of the properties and lousy paper they have acquired back onto the market and create the final real estate bottom.
(Hey, it may not happen, but it is probably as good as anyone else's guess.)