Then there are various typographical and layout features – at a very minimum cursive, bold and possibly underlines should be not that uncommon. Quite a few books use footnotes, which are a bit of a paint to represent in a plain text format that's lacking the ability to explicitly link footnote symbols with their corresponding texts. (So you either need to introduce hard pagination, or convert them to endnotes, neither of which is really satisfactory.)
Sometimes the pagination is explicitly played with, so even if your digital book doesn't use hard pagination, it'd still be useful to at least being able to force a new screen page.
Font sizes occasionally get used for creative effects or to otherwise convey meaning, and the same goes for font selection itself. Sometimes even colour is used.
And some books get quite creative in with playing with layout and typography effects. The Raw Shark Texts had some ASCII-art style pages, but utilising a proportional font (!) [1], and House of Leaves went totally bonkers in its use of creative typography (https://www.google.com/search?q=House+of+Leaves+typography&t...).
[1] Even if those were based on a fixed-width font, you still need a way of indicating to the e-book reader software "Hey, here's some ASCII art, please don't reflow the text here and don't put a page break in the middle of the art, either". With a proportional font you either need to make sure the exact same font you used for layouting also gets used for display, or just give up and include that text as an image (and an appropriate alt-text, especially if the text for the ASCII-art isn't just random gibberish, but actually meaningful text, too).