The Kobo and Kindle are functionally identical in terms of hardware, except for a few things that are specific to Amazon. But Amazon has been increasingly hostile towards Calibre in recent years. It used to be supported almost natively, but it seems like each update from Amazon locks down something that used to be accessible, or breaks existing functionality.

For instance, you used to be able to edit collections directly in Calibre, but Amazon broke that because they want everyone to use their collections (which are only included on books purchased directly from amazon) instead. So for instance, if you uploaded the entire Harry Potter series, you used to be able to tag all of them with the series and they’d be added to a collection together. You can’t do that anymore, and have to add them manually one by one on the Kindle’s laggy touchscreen.

They have also started breaking included cover art, because the Kindle automatically polls Amazon to download art instead. And when it doesn’t find any, (because the book isn’t from Amazon,) it wipes the included art instead of just falling back to it. Luckily this has a fairly simple fix (just unplug your kindle, let it index and break the cover art, then plug it back in so Calibre can push the cover art back to the Kindle,) but that means you need to actually take the extra time to do that every time you upload something new.

The Send To Kindle email functionality has recently been broken to where every .epub file you email just gets sent to Documents instead of Books or Newsstand. So if you have Calibre set up to grab news every Sunday, or to send new books to your Kindle, they won’t actually land in the News or Books sections like they’re supposed to. The only way to fix that is to plug it in and upload them via USB. Additionally, they have the same issue with broken cover art. So you need to plug your Kindle in to update the cover art, even when emailing your books. Which kind of defeats the purpose of emailing them, because you’d most likely do that if you don’t want to plug your device in every time.

The kindle’s indexer also has some weird issues, where certain books will just crash it and new books will stop appearing entirely. And there’s no way to see which book is the issue. So if you uploaded a bunch of books to your kindle, you’ll have to play guess-and-check to see which one is the issue. This may not be exclusive to the Kindle, but I haven’t experienced the same issue on the Kobo.