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You can change the title metadata on both Mobi and ePub.
As to better file formats. Mobi is a very old format that doesn't quite have the flexibility of ePub or the Kindle's more modern AZW3/KF8 format. Any of them will work just fine, especially for a typical novel type book, but ePub & AZW3 include more styling possibilities and also the ability to do things like embed fonts.
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