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Kobo is most open. It comes rooted. You can install Koreader on it which is very good at reading PDF.
However, Onyx and Likebook are Android, which means you access to A LOT more software. If you want to do out-of-the-box type things, if you want a very flexible device, go for an Onyx or a Likebook.
Onyx is better than Likebook for reading PDF because the included reader app Neoreader allows you to split pages into panes. Also allows a lot of control like pan and zooming etc. Onyx software is better at reading PDF than Likebook software. It is better than Koreader. But you can also install Koreader on Android. Also, in my experience the hardware is tougher and more long-lasting. Also the OS is more stable than Likebook, but Likebook has likely improved since I had one several years ago. But Onyx is a solid machine. But Onyx has no SD-card slot.
On a down-side, Android OS devices battery life is much smaller than a Linux device like a Kobo.
If you want flexibility, go Onyx or Likebook.
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