Ooh, I would love a Proteus storyline (or for that matter any storyline that used Moira better than XMFC). I haven't read the Ultimate version but the mainstream one really was good. Speaking of "Charles being a dick", did you read Whedon's storyline about the Danger Room?

Assuming that XMFC is considered as part of the same canon as the previous X-Men movies, Charles's behavior that is revealed in X3 shows him to be a character with deeply problematic ethics. So I sort of choose to believe we are intended to read him that way in XMFC and in subsequent movies.