(Here I’m fortunate to be a member of an academic institution, making most publications free to me, but I recognize that paywalls will be a barrier for others.)
Academic papers are almost all available in PDF format already. In DEVONthink, it means I can use the markup & annotation facilities on archived pages. I have technical experience with web archiving, know well many of its strengths and limitations, have written software to do it, and still (perhaps surprisingly) have concluded that snapshotting web pages as PDFs is the best archiving format for me. I save all web pages as one-page PDF documents. I now view my Kindle and iBooks collections as sunk costs, and am actively looking to replace all of them with copies in PDF format. I’m much happier reading and marking up PDFs. For me and how my brain works, though, they are sorely lacking in many respects. Lots of people feel the ebook formats have advantages, e.g., because they can be read on alternative devices, and I respect that. 
I recently reached a turning point, and gave up on ebook for anything that I’m going to study or want to annotate – basically, anything other than books for pleasure reading. I have many dozens (maybe hundreds by now) of books in Kindle and iBooks. I’m the same way, so would like to contribute some experiences. I would like to keep as much of my literature processing/annotation in DT as I can
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