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Originally Posted by stormdelta
So far I've looked at the Kobo Glo, Kobo Aura HD, and the Kindle Paperwhite. The Kobo devices look great, especially the Aura HD, and it seems like they have better support for PDFs in their software. Unfortunately their sideload support seems to be fairly weak - as I understand it, you can't even sync stuff to the device unless it came from the Kobo store, and I saw reports that you had to update the devices database after transferring over USB.
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Can I ask exactly what you mean by "sync", here? If you just mean putting books on a Kobo device, you can do that with Calibre via USB, or via the Calibre content server over wifi, or via Dropbox and the builtin browser and wifi, or by the other dropbox-style service of your choice, so long as it plays nicely with the rather rudimentary browsers you find on eink devices. (Another way of getting books on without digging out a USB cable is to use a micro SD card.)
I'm not sure what you mean by "you have to update the device's database after transferring by USB" - this happens automatically in normal situations, no user intervention required. Calibre can also manage shelves on the device, which is truly handy.
Now, if by "sync" you mean syncing bookmarks across different Kobo devices (eg to keep your place in a book between your eink reader and your Kobo app on your smartphone, and your iPad, and so on), then yes, you can only do that with Kobo books.
So that might not actually be an issue for you. However Kobo doesn't do PDF reflow, which might be a dealbreaker for you. Check out the Sony devices for that. Or test the sort of PDF you might be using on an Aura, to see if you can deal with it. But honestly, if you do a lot of PDF reading, and those PDFs include diagrams and fancy formatting and such, you are very unlikely to be happy with a six or seven inch eink device - a tablet is a fair better tool for those.