Because Burton thought it worked better that way.
He explained to BuzzFeed:
We switched Emma and Olive's afflictions, or whatever you want to call them. But luckily we had Jane, the screenwriter, [and] we ran some [stuff by Ransom Riggs]... you know, the author is still alive! He was a good collaborator. We just sort of felt that having Emma floating would be a bit more poetic and it was in the spirit of the book. So it just felt for the movie it was a better way to go with it. Because often times in novels, characters get omitted, deleted, condensed and I think Ransom felt confident that whatever changes we made were still in the spirit of the book and so it all worked out very well that way. There was no big fights or tensions or controversies in terms of how that came to be.
With the Authors blessings.
The actress for Emma thought the same, as it allowed the film to stand apart from the book while still being true to the spirit of it:
when I sat down and thought about it, I was actually really glad that they gave me the opportunity to create a whole new character because if you try to exactly replicate a book as well-loved as this book, you will never please everyone. So you might as well make an adaptation of the book."