epub.
>An EPUB file is an archive that contains, in effect, a website. It includes HTML files, images, CSS style sheets, and other assets.
Search works just fine on ereaders.
The flexibility of html is that you can render it however you want, for whatever viewport or feature. If you want pagination, just render it differently.
>But if you read longer documents you want pagination
For long form works, I do actually prefer having them on my kindle, but that's because I don't want to read long-form text by staring at a screen, and I want a lower line width. PDFs tend to be worst case scenario there, because they often render with the assumption that you're trying to read it on standard letter paper.
Also, we've had "pagination" for text files for decades. It's called "less".