[Negativedark]

A lot of what happened in Rebuild may have been because Anno has changed since he did the original Eva. As I understand it Anno was in a very rough time in his life when he did the TV series. I've heard he's a lot less depressed and upset now. It's also possible that is why he's changed the charecters. He may not relate as much to the persoanlities of the tv show and has changed them accordingly.
About the merchendising aspect. I don't think Anno controls that. While he made Eva, he doesn't really own it, I think mostly Gainex, Star King, and Sega do. I have however heard that he insisted they let Eva be put in Super Robot Wars, although I don't know how accurate that is. Also if I remember correctly When Gainex was first formed, didn't they pride themselves on bieng Otaku? They did make Otaku no Video.