You can change fonts in the Books app...there are 9 to choose from (on my iPad mini). I agree that the Kindle and Books apps are low on customization options compared to the third party apps.
I like the look of the Books app the best...but read in FBReader for most epub due to the extra configuration ability. I even liked it when the iBooks app tried to look like a book, complete with curled paged turning. Sure it was a gimmick, but I liked it.
Unfortunately, the DRM on Apple's books hasn't been broken yet. So, other than a few books, I don't buy or read Apple books. I buy Kindle books, remove DRM, then read via FBReader.
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