I'm also an intending-Kepler-Pro-buyer, and a big fan of Terry Pratchett (who was somewhat infamous for his humorous footnotes), so I'd also be curious as to how different Android eReaders (particularly FBReader) cope with eInk and footnotes.
One point I would bring up is that Onyx tends to have an optimised-for-eInk reading app (based upon FBReader, last I saw) pre-loaded on their devices. Admittedly, the version on my old (pre-Android) i62HD has broken footnote handling, so some scrutiny even with this may be advisable.
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