Beyond that, having to convert is another step. Sure, it only takes a couple minutes in Calibre. But after a few hundred books, it adds up.
So does the file size. I guess epub uses a better compression, they are usually only about 70% of the size of a mobi file. Again, not an issue on a case by case basis, but after awhile it adds up.
And simply working with epub is a lot better than mobi. Spot a typo in an epub? Fire up sigil and fix it. There's nothing like that for mobi.
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