My opinions:
- There's no real way to realistically put Raphael or a Raphael-like figure in the middle of Crono & Marle, so I wouldn't worry about that. Feel free to prove me wrong ;D
- Likewise, there's no need to go over the top with the whole Tree of Knowledge stuff. I would simply bear in mind that this card is connotative of Adam and Eve, and depict the two in some state of, I don't know, pastoral happiness, emphasizing the connection between the two. If you want to put in the symbolism, maybe an apple tree can be part of the scenery.