PDFs were not designed for eink readers. It is extremely difficult to implement a good rendering on an eink device, just because the way they work.
The closest thing I've found to a good PDF reader is the iPad using GoodReader app. You can do annotations, highlighting, notes, remember last page, you will get a full TOC or if absent, you can create it. You can jump between chapters in seconds and extremely fast turning pages.
Yes, it is not eink, it's a tablet, but that's the trade off. Besides, 10" screen gives you more display area avoiding zooming and panning; I barely need those when using the iPad. Any reader below 10", you will probably need landscape or any type or zooming feature, specially with tables or images.
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