Hmmm......maybe the Snake and EE thing is when Raiden was fighting Vamp and Snake picked her up to take her to Otacon, but on the way there, there might be some things that happened. This could be just another bonus mission for Snake, to see if he could deliver EE to Otacon safely? Or, maybe for the new game, EE is telling Snake something about Raiden and her that was unknown to us in the MGS2, because Raiden was fighting Vamp. I hope I'm making a little sense....
As for Raiden with the blade in the Tanker chapter.....I'm confused about that too. I wonder if this is something like the Japanese version of MGS2: Where you get to switch the characters to play in any chapter you want?
Snake and Vamp: Maybe instead of having Raiden save EE, Snake is doing it instead while Raiden is off doing something else. Like they swapped missions or something. Or maybe Raiden got injured and Snake had to take over for him. I'm not sure....
Maybe my guesses are really silly, so sorry.
