well. this has been developing in my head most of today, so here it is.
Everyone thinks Richard is behind it. Now, Richard is most likely behind Carnage's return, as his "concern" for Gwen implies. But the flashback shows him working on his research. So I doubt he stopped on that to make clones of his own kid. SO if Richard was only working on Carnage, then who is doing the cloning?
More on that later.
Now here's the deal with Fury. When he got to be head of SHIELD, no doubt there were others wanting it too. Gyrich was probably one of them. Now, there was a choice between Fury, who saved the Pres. with only one arm, and Gyrich, who is in charge of the creation of a monster like Carnage. Who do you think got the job? Fury. So Gyrich gets more than a little pissed and decides that Fury may not be exactly a boy scout. There has been some proof pointing to this, and only just enough for Gyrich to get the CIA's own meta-human program going on. To counter SHIELD, and just in case Fury goes rouge. Yeah, like that's all Gyrich is concerned with. Anyway, he gets Richard because of his Venom research. But it seems Gyrich takes an interest in Spider-man, who seems to be a genetic wonder. He discovers that it's Peter Parker, Richard's son, go figure, and that Fury has gotten to him. At the same time, he confiscates some of Connors' work. Remember, Doc Connors went to the Feds, not SHIELD. Now Richard has enough to seriously start work. But then comes Ben Reilly, who happens to be working for the CIA( the whole, more secrets of Ben Reilly thing). Reilly and Parker work on Carnage, Richard probably considering it's positive attributes, like being a cure( to DEATH maybe???). But Reilly has Parker's bloodsample. He gives it to Gyrich, who sees that he's got a sample of gene wonder Spider-Man. Since Fury has the real Spidey, the onlt thing to do is make your own. Except not have only one, but FOUR!!! Now, it could be anyone who does the cloning. Reilly, Richard(doubtful) or maybe some other scientist......maybe Miles Warren?!?!
Next point: Gyrich would probably want other scientists working on things to counter Fury. And he has a spider-clone, but it should be even more powerful than the original. I give you......Scropion!!!! All the powers of the original but with a little extras! Namely, an illegal bio-graft. And WHO do we know that has played around with bio-grafts?? That's right, Doctor Octopus. Now Otto is considered less of a danger since his arms have been melted. So Gyrich makes a deal with him. Work for him and he won't be stuck in high-security vaults with other psychopaths. He takes it and Fury can't do a thing, since the CIA has given the go ahead. So Ock is working on some little gadgets, such as Scorp's tail. But do we trust him? Nah, of course not. He is probably building himself some new arms, and just completed them when he says enough is enough and goes after Peter(hence no coverings).
Well, ther you have it. I thought up more, but this is huge, so......nuff said.