The problem lies not with the reader, but with the PDF format. PDF is designed to be a reproduction of a specific-sized printed page; that is a task which is does extremely well.
The issue is that a 6" Reader has a 9x12cm screen. Cut out a piece of paper that size and compare it to a page in one of your books. You'll find that it's a lot smaller.
There's just no good way to reduce the size of a PDF page. Some pages can "reflow" to handle a smaller screen, but it's a "hit and miss" affair and, especially with complex technical layouts, very often just doesn't work at all well.
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