Some reasons for using a new format instead of an existing one:
1) Existing format(s) might not support some necessary features (e.g. mobi and fonts).
2) Using an existing format might require an expensive license, or the format owner might refuse the license
3) Using a new format allows the company to fully control its development and not rely on someone else
4) Using a new format allows the company to control its use (e.g. implement/change DRM, charge for the viewer program etc.)
I guess in the end it's most probably going to bite them in their backs but a lot of people are not able to see beyond the immediate gain.
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