XDD you made some very good points and i can see your logic. In fact, I'd say that's the best case yet!

although in point 2, you made it sound almost as though the Noah is equal to Corruption? Ie, he has lost humanity, he's (full Noah) Corrupt. But from later on, I can see what you meant, but the idea is interesting. What if, over time, not their thoughts or goals or intentions have been corrupted. What if the very existance of a Noah IS corrupted? What if the Noah gene has adapted to those ideals (point 3)

As much as I like your theory, I cant get my head around Allen not being Allen. (even though Allen is actually Red, who kind isn't after what Allen's been through, you know? XD)
Although, before this fanfic, I couldnt consider Neah just leaving?

anyway, I'll add to this later (maybe!)

[internet troubles -.-"]