Part of the ending that I like, not because of this, but [BLACKOUT]part of the ending that I like is that Lex completely changes his ways even though he is sentenced to death. He isn't trying to get out of it, he knows he will die and soon. He has accepted his sentence, but he still helps from his cell. For him to be Leo, that would mean he didn't die. Somehow that takes some emphasis out of his change for me.[/BLACKOUT]
Not saying that the comic shouldn't or didn't imply that idea, I'll have to read it closer some time I guess.
In the book Lex isnt sentenced to death. The narration boxes tell us that without Superman, Lex fell into obscurity. "What happens when an unstoppable force meets an immovable object? They surrender."
So that is the official ending for Lex in the book. But if you look at the clues then you might buy into the Leo theory, as in Lex repented and went into the past to make up for his evil deeds. "If you wanted to do good, you would have done so years ago" Superman tells Lex.
And in the end Superman makes the formula for his reproduction with Lois himself, giving it to Leo before he flies to fix the sun.
- You trust me with this? What if i was the devil?
- I think i'm a good judge of character.
From this scene we get the following:
1) Why did Leo say that if he was an ally all along? If he was Lex, then yeah he has been helping all this time, but to be trusted with Superman's lineage? He must have been surprised to see Superman trust him that much. In other words why would Morrison make such a big deal out of this? Would Lucious have asked Batman that? No, because he is a de facto ally.
2) Superman and Clark have been trying to "save" Lex throughout the whole story. Superman tells Leo that he is a good judge of character, so he must have known about Lex's potential to be trying to save him all along. Not only that, but SM can use his microscopic vision to read DNA strands, so he must have read Lex's DNA in Leo. The thing is that SM believes in him, like he believed in him all along, even when he was Lex.
There's also the scene about Lex's monkey called Leopold, dressed in superman's suit to mock him, so what a better gesture to show his true remorse than to take the name of the monkey (Leopold = Leo)? The scene was omitted in the movie because it served no purpose, since Lex got a different ending.
The monkey having the same name as Leo, Leo and Lex wearing the same coats only with different colours (Leo's rainbow coat symbolizing what he saw with Superman's powers perhaps?), both holding their hands behind their backs, Leo being suprised with Superman's trust, etc are clues that they are the same person.
Not only that, but the ending of Red Son was Morrison's idea from when he and Millar were pitching a Superman retcon to DC and he let Millar use it in Red Son, and it is believed that he wanted to surpass that in his Superman epic. And he surpassed it indeed, with Superman achieving the ultimate moral victory, by changing and therefore saving Lex. Superman is a super-jesus in the DCU, but seeing him become that for his ultimate enemy? This theory makes for probably the best, most uplifting and heart warming ending to SM and Lex's rivalry and its too good to just be a coincidence. There are no coincidences with Morrison.
Finally, Morrison loves time traveling stories with people going to the past and being responsible for things we see in the present or future, plus he is well known for his uplifting and optimistic endings. DC One Million and Return of Bruce Wayne are testaments to that. Even the All Star chapter about Pa Kent is a testament to that, with present Superman masking himself to go back to the past to see his father one last time.