I'm another that much prefers Kobo readers over Kindles because of the fine-tuning possible for fonts (I have a PW2 as comparison which I never use).
Kobo lets me add my own fonts, has settings which darken and thicken the font, both important for my crappy eyesight, lets me adjust line height and margins, and Collections are automatically handled by Calibre. Kindle fonts are too thin and I can't add my own, they look gray in comparison to the Kobo, line spacing and margins too big for my taste, and unless I want to manually set collections for each of my books, Calibre can't send collection info to Kindles. Kindles can no longer be rooted without opening it up and using a serial connection, more trouble than I want to go through for every firmware update to be able to use my own fonts and collections.
I don't read magazines, I only highlight when it's a correction that I want to make, and I rarely encounter footnotes. I don't read PDFs, other than having a few maps on the reader that I might need. If I ever need to, I much prefer a larger screen for PDFs.
It all gets down to what's important for you on your reader.
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