Even if you remove Stephen, there are still problems for Matilda. Until August 1136 her pregnancy realistically prevents her from travelling to England to be crowned. Stephen's elder brother, Theobald, also has a strong claim to the throne, which would receive the support of most of the Norman barons, and probably a lot of the English ones if he makes it there (there's another elder brother, William, but it's believed he was mentally deficient).
Matilda's best chance of being declared Queen would be for Henry I to hand over the castles in Normandy to her before his death, as she had demanded, in order to allow her to build up a power base their. Then, if she doesn't become pregnant by the time of her father's death, she can travel to England to receive the crown. She can rely on the support of her half-brother, Robert of Gloucester, which is a position of strength to be working from. Even still, Stephen and Theobald could cause her problems, especially if either got to England first.