From my perspective, the clues seem to be building each issue towards the inevitable conclusion that the Justice Leaguer behind the secret American government superhuman program is....
drumroll...
Professor Martin Stein, the second half of the Firestorm matrix. When we first met Stein, he was a nuclear scientist. Perhaps the "accident" that created Firestorm was originally meant to empower Stein, but Ronnie Raymond became involved and ended up becoming the consciousness driving Firestorm. This would play into the idea that Ostrander had already established that Stein was the intended host of the fire elemental that became Firestorm.
Furthermore, most of the villains revealed to be secret government agents have been part of Firestorm's rogues gallery. It would also make sense that, if Luthor is indeed correct and the person behind the Superman Theory is a member of the JLA, then we've probably already seen them. Aside from the brief cameos by Superman, Batman and Firestorm are the only Justice Leaguers who have appeared in Doomsday Clock.
Anybody got a better theory?
(Oh, and if you are about to comment in this thread just to chime in about how much you hate Doomsday Clock or to complain about the delays, please don't. We are all well-aware that some of you don't like this story. We don't need a reminder. Thank you.)