I'm guessing she will be mostly pertinent to the story mode, sort of like half the batsuits from Lego Batman 2 became unnecessary after you unlocked all the characters. Maybe she'll automatically morph into the character you need for a given puzzle, or maybe her morphing powers will just be limited to the other characters in your presence if you happen to need two of the same power or something.
I get the impression that her powers will be limited in some way though, maybe she'll only be able to morph into the X-Men, who knows. If she can transform into any character on the fly by quick toggling the same way we already can in freeplay with R1/L1, that would pretty much render every other character redundant, and you'd only need to play as Mystique.
In fact, if they stayed true to the comics, she shouldn't even be able to copy their powers, just their appearance.