I like that Ultimate Carnage seems to be pretty different in origin to Ultimate Venom. After all, the purpose in creating Carnage in 616 was to replace Venom as a villain since he was being turned into a hero-of-sorts to capitalize on his huge popularity. Making Kasady a serial killer before becoming Carnage was, i believe, mostly to stop future writers being tempted to turn Carnage hero as well.
But Venom is still such an unexplored character in the Ultimate U. He has only fully appeared in 2 issues and his current status was left unconfirmed (although #39 comes close to confirming him to be alive), so there's no need to bring in a "replacement", or a "substitute".
And if it's true that Bendis was watching/reading about "the do's and don'ts of genetics" when he came up with his idea of Ultimate Carnage - a character who he had no interest in writing before - that kind of idea should definately be capitalised on, rather than trying to make him the same as Venom just because he's the same in 616.
Unlike Venom, though, I think we'll see a pretty convincing death for Carnage.