Again, this is an artistic complaint. Personally I don't see much difference in Kaine's appearance in this and 'Lost Years'. They both look like scraggly, dirty bums with Alan Moore-style hair. But if you see a difference, that's your take. However, that can't be blamed on Guggenheim.
Also to your earlier point. Kaine is NOT an exact copy of Peter like Ben was. He has the same basic genetic code, but he was twisted and abused by Jackal early in his life and never given Peter's RNA code which had Peter's memories and ethics. The degeneration, twisted powers, early abuse and lack of RNA coding all led him to become what he is. Ben was like Peter in every way, except for five years on the road. Kaine had many more differences, not only in his experiences, but in his construction. If he showed signs of physical degeneration, maybe he has mental or emotional degeneration too.
I suppose one could pass this of as an artistic complaint, but since Guggenheim went back to pull the Dr. Epstein reference, he could have also noted Kaine's state as of that series, he got really bad in issue 2.
Yet for some reason he is fine by the past events in Who was Ben Reilly. I understand this is a minor artistic difference for you, but it's a little more than that for me. I get that Kaine's appearance was never really consistant, after he got his regenerative suit and all, but it seems like he should have been way more messed up in this new arc. As for his appearance in Web of Spider-Man 1, at that point who knows exactly when it takes place, or what the scientists have done to him.
As far as the RNA... DNA... all of that... I mean I guess I can see what you're saying (though I don't totally understand it) the point is that none of that is explained in this story, we simply know that Ben and Kaine are clones of Peter. Peter decides that Ben couldn't be a murderer because he had the same DNA. Which is also shared by Kaine.
I mean you can explain it away all you like to yourself, we all have our own opinions, we can't change each others, but I think Peter's whole reasoning for believing Ben couldn't have been the killer was a realization he could have come to in say that last panel there in the Annual. Did he really need three issues to be like, "Nah, Ben is a good guy."
The reader always knew Ben was essentially Peter, just stripped of Peter's life and allowed to grow on his own a bit. The worry was that this story would attempt to change Ben's character in some odd way. It didn't... fair enough, but the fact that the guy killed his OWN family and went on for years hunting Ben/Peter is a little weak. I mean, if someone had posted, after that Annual had come out, "Don't worry guys, it turns out Ryder murders his own family and blames Ben." I think we'd have all wondered why the hell bother with the story. Guggenheim had a great idea with having a villain come after Peter, not for being Spider-Man, but for something he thought Peter did, it was just poorly (in my opinion) executed.
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