It's odd how they are doing this new Clone Saga, saying that it is essentially how the Saga was originally supposed to be before it was dragged on. Well, Traveller and Scrier were right there from the beginning, and they are no where to be seen in the updated version, so obviously for time and pacing reasons, the crappier parts are getting cut out. The interesting part about Scrier and Traveller is that they were a part of the Clone Saga from the beginning, and obviously were supposed to be a huge part... clearly not so in the retelling. Obviously after the huge amount of retconning they used on Traveller and to some extent Scrier made them too much to even try to work in to the Clone Saga update.
As for the blonde hair, I don't think it was ever the intension to have him distinguish himself visually from Peter, as the original plan was for Ben to just take over as Peter... but as Ben was taking over the Spider-Man mantle, Budiansky told the writers and artists to have him dye his hair to give Ben his own look. (This is in Life of Reilly)
So clearly in the New Clone Saga, they are streamlining to just the Jackal plot points, with Norman Osborn in the background, revealed at the end, unless they attempt to switch it up and make it Doc Ock or someone. I doubt they will do that since Ock probably won't be in the Clone Saga, nor will Grimm Hunter, and Kaine will have no edge. Also, the pinnicle of the Saga, the death of Aunt May, probably won't have a fraction of the emotional impact it did in ASM 400.
Anyway, at this point I'm just speculating shortcomings of the series. We'll just sit back and see where it goes.
In regard to the current continuity stuff, I did like how in Web of Spider-Man they stated that Ben was the best of Peter Parker, while Kaine represented the worst. It was a good dynamic, and just made wish Ben was back.