All my 'needs' are met so here are some wants. Rendering pdfs was solved long ago, so I'm not sure what distinction you see between Mendeley and 'the reader itself'. It's been a while since I used Mendeley, but it wasn't perfect.<p>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].<p>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.