Well, I think that by the end of FC at least, young!Mystique has made some big strides in getting over her insecurities. And she might be a tad naive, but no one can stay naive or innocent for long hanging around a guy who basically runs a terrorist cell. And even in FC, she already shows that she feels quite bitter about the world that won't accept her, so it's not like she's some happy-go-lucky girl.
But as far as cold hard manipulative b**** characters go, I think that Emma Frost would be the one who could fill that role more naturally, at this time. Now that she doesn't have Shaw to simper around, I hope they allow her to be more assertive.
As far as reconciling FC Mystique with original Mystique goes, it's not that I can't believe that FC Mystique could ever become a cold hard manipulative assassin. It's more that the way the character is handled and presented is so fundamentally different. In the original series, Mystique is little more than a henchwoman - basically a version of what Emma Frost was in FC, except with even less lines. This kind of character usually has a limited role and does not really demand a detailed characterisation or dialogue. In FC, Raven/Mystique is one of the lead characters and lead characters are supposed to be much more fully realised and can't stay virtually mute. So the jarring effect for me is in the way Mystique goes from a lead character in FC to a flat henchwoman character in the original movies.