Relationships:
Raphael and Amy - Partners: The commitment Raphael shows to Amy is seen by some as a more than just fatherly. Their relationship seemed to start up very quickly, from her doing a good deed to her "becoming an irreplaceable part of Raphael's life" which does cause suspicion to some. Some people do also enjoy the pairing of Amy and Raphael, insisting that as the two of them aren't actually related and so the relationship could develop as she gets older (see below for ideas about Amy's age). So perphaps their relationship could develop as she ages, as in Setsuka's story, where she fell in love with the man who raised her. It may seem a little distasteful, but who knows.
Raphael and Amy - Unrequited Love?: The one thing that really struck me when reading Raphael's story was the very end where it states Amy "betrayed no hint of what lay hidden in her heart." This originally suggested to me she may want to go against what he was doing, but on reading the brief story for Amy, it tells us she supported him. Was the desire to help him? If it was why was it hidden? This does suggest something a little strage to me, perphaps not that Raphael has romantic feelings for Amy, but maybe that she does for him.
The Sorels and Kilik - Friends or Enemies?: There is a link between Kilik & Amy, possibly Raphael too. As he heals her in one of the ending's to Raphael's story. To me, this paired with the information from Amy's story, seemed to suggest stronger feelings for Raphael than I had previously thought. She merely looks down at the floor, then out of the window when she is healed, coming across quite forlorn. She gives a much more positive response to Raphael's return. Some seem to think that she may have feelings for Kilik, which I really can't see. Before I knew of the information in her story from the Japanese website, I thought it possible she had wanted Kilik to heal them both, but instead I now think she would dislike him for healing her, taking her away from and ruining Raphael's world.
Others from Raphael's Story: It's hard to say there are any other relationships in his story, but he obviously has connections with Siegfried/Nightmare. I guess the only feeling Raphael has to them is resentment and hate. He is also one of the common people to encounter just before fighting Nightmare or Siegfried, although he appears in quite a few people's stories towards the end, I don't see their being any real links between them. They tend to just "see what he is doing as wrong".
Pairings Anyone?: My ideal pairing is Raphael and Ivy, although improbable, I think the two of them suit each other. This is all I can really write about this for now, as I don't read all that much fan fiction. If anyone has their own analysis of a pairing, I shall post it.
Raphael and Amy - Father-Daughter: I personally see no more to Raphael & Amy's relationship than a father-daughter relationship. She is also said to be the only one to show him such kindness, so it is possible he felt feelings of gratitude and liking he never had before, having also previously been a bit of a 'loner'. To put it bluntly, I really can't see the idea behind Raphael being a paedophile, he is merely a created game character and it's difficult to see why any creator would do that. If it was real life in the modern day we may be a little more suspicious, but as it is just a game we can assume the intentions were innocent and that there really is nothing more too it. It may be possible a relationship could develop (see next paragraph), but I still think it's unlikely. Perphaps the creators were a little niave to how some in the western world would interpret the relationship.