Well
Ungrateful Daughters by Maureen Waller (fantastic book on the family dynamics of the English royal family leading up to the Glorious revolution and into the reigns of the last Stuarts) mentions the health of Queen Anne's eldest daughters (Ladies Mary and Anne Sophia), and the results of their autopsies after their deaths from smallpox. "
The autopsy showed that the elder girl was 'all consumed, but the younger quite healthy, and every appearance for long life'." So while Lady Mary's health was quite fragile and wouldn't have likely lived much longer (even without the smallpox), the doctors seemed to have believed that Anne Sophia had a good shot at a long life. So an Anne Sophia that never gets/recovers from smallpox would most likely succeed her mother as Anne II in 1714.
@Kellan Sullivan is absolutely right about William, Duke of Gloucester though. Looking at his brief life and his major health problems (he is believed to have contracted meningitis at birth, definitely suffered from hydrocephalus, and couldn't walk up stairs unattended at age five, to name a but a few) William was on course to be Britain's bewitched King. Now even without the meningitis, its hard to guess if Gloucester would be healthy or not, but considering the fates of the majority of his siblings (stillborn, miscarried, and died after a few hours), his chances aren't great.
@What if , there's no legal way to bypass Anne in favor of her son. Gloucester's claim came from his
mother, therefore she would
have to come ahead of him in the succession.