Personally, while I'm not expert on Arthurian tradition, I wouldn't go as far as to say Morgan le Faye was evil or anything. You're right to say that she's not necessarily good, but I don't think she fits into the evil category. And the Green Knight is symbolic of a lot, and I do mean a lot, of things, but he's certainly not evil.
Anyway, ask and you shall receive. I shall "enlighten" you, though I would never use a word like that to describe giving examples to support my opinion. First of all, there is the big and obvious connection of the Geass. The Geass impacts Lelouch, Rolo, V.V., and Charles (Mao is in there somewhere, too). That is a common thread between all of them and, as a result, shows that C.C.'s story, in some way, affects them. Let's not dismiss the fact she speaks to Lelouch's mother and while that is a bit of a mystery, Lelouch's mother is a HUGE piece of Lelouch's story and her being able to speak with her puts C.C. right in the middle of that plot. I am just going to list two of the major and more obvious things for you, I'll just have to hope that suffices as enough "enlightenment" for you.
I also think you're looking at everything at face value, which doesn't surprise me considering your clever ability of seeing, hearing, and reading what you want. C.C.'s influence on events doesn't come right out and smack you in the face, they're hidden from us, the viewers. Obviously, this is speculation and there are no hard facts to back up the idea that she's affecting things, but one could logically infer that. Just as, I suppose, someone could logically infer that C.C. doesn't matter to the story...of course, that would probably be the same as someone who was reading the play
Macbeth and saying, "Oh, that Macduff...he doesn't really matter anymore!" But then at the end of the play, you're blown out of your seat because Macduff is the one who takes Macbeth out.
Sometimes, when you post, I have to remind myself that you're only like, 12 years old.