And now - all of that had to be reversed again in order to make Peter Spider-Man once again, and Ben the clone. But how? If you read the one-shot 101 Ways to End the Clone Saga, you get an idea of the quandry Marvel found themselves in since they had let this monster get completely off-tangent. They either had to create some huge cosmic event, some new fangled scientific oddity or come up with someone big enough, bad enough, and around long enough, to have been pulling Miles Warren's strings from the very beginning. Not only that, but it had to be a Spidey villain who knew that Peter and Spider-Man were one and the same, and who hated them both to the degree that he would have the motivation to manage the events of the Saga. To have invented yet another new villain to have been behind all of this would have been a huge letdown, and any cosmic events would probably would have made the situation even more complicated and cumbersome to deal with in the future.
So, now you begin to see how limited Marvel's options really were.
Venom couldn't come to the rescue, because not only did the first Clone Saga long predate Venom, but Eddie Brock clearly did not have either the intellectual or financial resources to pull off the Clone Saga. Plus, it just wasn't his style. Doctor Octopus certainly would have had the brainpower and the access to the kind of science required - but he did not learn Spider-Man's secret i.d. until Amazing #397, and even at that, he had just been killed off by Kaine (another dumb move) right after he had made an odd sort of peace with Spider-Man.
The only other classic villain to whom this whole affair would have been feasible for would have been Mysterio, since he theoretically could have induced a super illusion on Spidey for the duration of the Clone Saga - but that would have required Marvel telling fans that the Clone Saga never happened.
So that leaves only two possibilities, and both have the last name of Osborn.
Now, Harry was a fairly probable candidate. In fact, I remember the owners of a comic shop I used to patronize speculating that the mastermind behind the Clone Saga was Harry. Perhaps he would have been a less controversial choice because he hadn't been dead for very long, and his death was not part of a widely revered story.
However, Harry didn't really work, either. For one, he had just been dug up and his identity confirmed in Legacy of Evil. (Not that would necessarily stop him from being brought back to life, I admit. After all, in The Jackal Files didn't the Jackal state that he had confirmed that both Harry and Norman were dead?) Second, during the time that the plot of the first Clone Saga would have been hatched, Harry would not have had the motivation or the wherewithal to have concocted such a scheme. In Amazing #122 he was recovering from another acid trip, and while he was coherent enough to have switched his father's clothing (and pay off the coroner in Osborn Journals), it would have been a bit much to have him be the mastermind behind the Clone Saga. Additionally, he did not confirm for himself that Peter Parker was Spider-Man until issue #134, and after being beaten by Spider-Man in issue #137, he went to the booby hatch where he stayed until issue #151 and by then he had forgotten about the whole Green Goblin gig. In fact, until Harry got his wits back around the time Bart Hamilton became the Green Goblin in Amazing #176-180, he was pretty much a harmless simpleton. Not only that, but he did not even remember that his father was the Green Goblin until the Hobgoblin tried to blackmail him with that information in issue #249. So, yes, it could have been Harry, but that would have required a lot more creative dancing and retconning that the choice that was finally made.
That leaves only one little indian - and his name is Norman Osborn, the only villain who (1)knew that Peter was Spider-Man, (2) had the financial resources (3) had the cunning, and (4) had the motivation to pull this off. After all, we don't have to be told how much he hates Spider-Man. In fact, Harry's recent death actually made Norman's return at that particular time even more plausible, and provided him with a significantly additional motivation to wreck Peter Parker's life.