One aspect between Kindle/Kobo that isn't mentioned very often is the device management, particularly for those who have more than one device per account.
With Amazon you can select which ebooks to download to which Kindle you own (and through the Archive access all purchased content and download additional ebooks from there).
Kobo appears to sync all ebooks to all devices, even previews. My wife and I have different reading tastes, and by having a Kindle each neither of us have ebooks flooding our devices which the other one has bought.
Lastly if you intend to also use an Android/iPod app in conjunction with your ereader, I personally find the Kindle app far less intrusive than the Kobo, and a little more polished.
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