If PDF use is at least fairly important to you then steer clear of both:
PW PDF review below:
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When it comes to PDF files, the Kindle Paperwhite is pretty much exactly the same as the Kindle Touch from last year. All the features are the same, with the exception of the new instant translations feature and the removal of text-to-speech.
The Kindle line of ereaders have never been a very good option for reading PDFs, and the Paperwhite is no exception. It’s okay for referencing PDFs occasionally but certainly isn’t something you want to use everyday.
The main reason for this, of course, is the small screen size. At 6-inches diagonally there’s not much you can do but zoom in on everything. With the Paperwhite there are two options for zooming: double-tapping and pinch-zooming.
Double-tapping shrinks the margins down to about a quarter of an inch on all sides, and pinch-zooming allows you to customize exactly how far you want to zoom in. When using zoom you can pan around the page and there’s an indicator that appears at the bottom of the screen and to the right of the screen that shows what part of the page you are zoomed in to.
With two-column PDFs, double-tapping automatically fits one column to the screen at a time, which is nice.
Zooming remains when turning pages with the double-tap method, but resets with each page with pinch-zooming.
One problem with double-tap zooming is the level is set automatically, and if there are any kind of variations in the text size or if there are diagrams or pictures from page to page or column to column, the zooming levels get messed up because it automatically sets for the different size and then doesn’t re-adjust for the rest of the page.
As far as features for PDF files go, you can highlight, add notes, look-up words in the dictionary, jump to specific pages, add bookmarks, switch to landscape mode, use the table of contents (generated by the Kindle), run searches, share on social networks, reference Wikipedia, and get instant translations just the same as with regular Kindle ebooks.
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http://blog.the-ebook-reader.com/201...-review-video/
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When it comes to PDF files and comics, the Kobo ereaders are rather basic and don't offer very much in terms of features. There's a zoom dial for zooming in and out, no presets, reflow, pinch-zooming, or advance features whatsoever. Not even any of the typical on-screen features work. No notes, no highlights, no dictionary. Nothing.
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http://www.the-ebook-reader.com/kobo-glo.html
The PW is the winner, but given the choice here, that isn't saying much.
EDIT: I know this is contrary to your specification, but do consider getting a 9.7 inch e-reader device like the Onyx M92 (the best for academic uses); otherwise you will be stuck using the PW in landscape mode for PDFs, and even then it may not work for large PDFs.