I often read books in PDF format, sometimes novels but most often academic texts. I often want to quickly look something up in another part of the book, and then return to my starting point. For example:
If the text refers to a notes section or an appendix or a references section, I will often want to quickly look at the corresponding part of the book, and then return to where I was.
If the book says something like "see theorem 2.8", I will often want to either flip through the book or search the text for "2.8", read it, and then go back to where I was.
If the book mentions an unfamiliar term, I might want to look it up in the index or the table of contents, then go to the page where it's explained, then after reading about it, go back to where I was.
In all the PDF readers I've tried, these tasks are possible but sort of awkward, requiring me to set up bookmarks and navigate my way through menus in a way that's a bit more fiddly than I'd really like.
So I'm looking for a PDF reader that's really designed around navigating the different parts of a book in an easy and intuitive way. I don't want to be too specific about how this is achieved, since I'm not a user experience designer myself, but one thing I can imagine is to have multiple tabs that can be opened at different places in the same book. That way, I could have one tab open at the references and another at the place where I'm reading, and then quickly open a new one if I want to look something else up.
Here are some more details of what I'm looking for
I'm mostly looking for an iPad app, but would also be happy with recommendations for Android or OS X apps.
The most important thing is a clean and intuitive user interface that works well for the specific tasks described above.
I often read PDF files that are basically scans of a book, so they don't contain hyperlinks or any other useful metadata like section headings; I'm looking for something that doesn't rely on those things.
I don't really care about PDF editing or document management features. I'm imagining an app that sees reading a book as its primary purpose, and does that job as well as possible.
One extra feature that would be really useful though is the ability to add notes to the pdf using the Apple Pencil. Ideally, I'd like to be able to draw outside the physical page, so that I don't have to cram everything into the margins.
I prefer free of cost (gratis), but don't mind paying a one-time price. I'm not interested in anything cloud-based or subscription-based.