I found a solution for the eBookwise disappearing dictionary problem, if anyone is interested! (
https://www.mobileread.com/forums/showthread.php?t=68172).
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Syncing only works with content purchased (or downloaded in the case of freebies) from the Amazon Kindle store. Sync will work across all Kindle reading devices (Kindle, Kindle for PC, Kindle for iPHine/iPod Touch and online at Amazon). You can also transfer those notes to a computer (they are stored in "My Clippings.txt" on the Kindle).
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Thank you daffy4u, this is useful knowledge. I wish you could extract notes from the eBookwise as easily as you can from the Kindle, that's neat. That is unfortunate about not being able to sync non-Kindle Store books, however. I guess I wasn't even sure you could put non-Kindle Store books on the device. Otherwise, the Kindle sounds great for writing papers and articles since you could easily reference all your notes using the Kindle for PC application. Although I'm still not convinced I would like typing out my notes on a little keyboard.
So in short, the Kindle would be perfect if it came down a third of the price, incorporated extractable handwriting/stylus notes, and allowed you to sync any public domain texts (with notes) that you put on the device. Right now, the eBookwise is a really good fit for me. I hope these folks give us another generation of e-readers.