Are you satisfied with current readers? What are your needs?
2. Ever tried to read/skim 100's of PDF's in rapid succession? (A common task if you are doing academic research.) It's near impossible. By comparison to reading text documents or viewing images, reading lots of PDF's is SLOW. Need a viewer that can view PDF's as fast as we can view text documents in pagers like less or images in viewers like feh. My suggestion: a viewer that extracts each page as an image and then views the PDF's as a series of images. (Essentially making reading them the job of an image viewer.) The trick is getting the sizing and resolution right, and dealing with hundreds if not thousands of extracted images.
PDF is great for printing. It also looks great on a screen (e.g. for casual, occasional reading, or presentations to an audience). But for reading lots of academic papers or any sort of document in bulk, PDF is absolutely terrible.
Postscript development is really an underappreciated area, I think. How does Apple achieve such lovely text on their displays? I could be wrong but I have always had a hunch their expertise in Postscript plays a role. They were once Postscript pioneers... remember the LaserWriter?
References would be best done a la Wikipedia, hover to see details, click to follow [the coup de grace here would be taking the pdf footnote text, extract a URL/search query, attempt to download a pdf, auto-parse it, file it, open it, browse back and forward like a browser, maintaining scroll position].
A scroll marker that helps you keep position, a la Readability. Better integration w/ file managers would be good, but replacing features is okay. Managing pdfs is a more specific workflow than managing 'files': a tree-explorer to see all pdfs in which folders (no other files), a tree of recently viewed items (+ nesting for reference-hopping, etc). All the auto-parsing magic (Title, Author..) is great but I would not reinvent it.
OSX: Skim (with an honourably mention to DevonThink) iPad: PDFExpress
Usually I should scroll down to the end to see references and then back to top to continue reading, life could be a lot easier if readers could parse references and show them in the sidebar or split the view so I could scroll down the bottom pane.
I can not repeatedly select a portion of text, move to toolbar, click on Annotation, select Highlight, in order to highlight a sentence! I wish readers had better support for keyboard or at least used modern UI/UX techniques.