ePub formatted books (if not DRM protected) are easily converted into the mobi format and vice versa.
Free online converters can be used, ie,
www.zamzar.com or with with free offline software, ie, calibre. Calibre is cross platform and is an excellent ebook manager for anyone.
Therefore the choice of an ebook reader on the iPad is not at all limited by the file format. For that matter, owners of Kindle, Nook and other reading devices are in no way limited either.