When designing an Articulate Storyline course that'll be viewed on an iPad, you'll want to use a 4:3 aspect ratio in order to make the best use of all the screen area.
The default story size of 720 x 540 is your best option. However, as long as you maintain a 4:3 aspect ratio, you can change your story size to 800 x 600, 1024 x 768, etc.
If you use a different aspect ratio, Storyline will maximize (scale) your content to fit within the iPad screen to prevent scrolling and provide the best experience possible.
See this thread in E-Learning Heroes for further discussion.