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"Academic PDFs" covers a lot of territory. Do you mean chemistry, or philosophy? I read a lot of PDF social science articles -- no pictures, in other words -- on my Kobo. I use Calibre to convert them to ePub. Results are anywhere from good-enough-to-read to pretty much perfect. Tables and graphs and stuff though don't really work. But I'm generally very satisfied with this pretty simple technique, and how the results come out on the Kobo.
I don't know about other e-readers, but the straightforward Windows file system access to the Kobo also makes it easy to manage these files. I tend to dump lots of them in haphazardly and then clean up later when I don't need them anymore. So it's easy to just use Windows Explorer or whatever to go in there.
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