I know that in Icons, Bash, or even Tri-Stat, most of the time, they advice to create two different psyche, for the two character have different personalities. Except if the character and the Super in which he turns into have the same mind and same personality.
In my first example of two identities (on page 1), I was more troubled with a character turing into a monster, but with the same personality, memories and therefore the same basic aptitudes, plus the new ones acquired, added to new powers.
Like if Doc Banner turned into the Hulk and kept his mind, his intelligence, his memories and most of his skills. In game terms, it would mean that the Hulk aspect would have more dice to dish out without bringing any real disadvantage to Doc Banner.
But maybe this kind of situation can be easily ruled by giving the player the same starting number of dice than the other players, and ask him to create two characters (Doc Banner and Hulk) with this number of dice.
Sorry for my English, but it's not my primary language.