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A lot of eReaders nowadays have Wacom touchscreens, run android, and have an unlocked bootloader.

Unless you limit yourself to mainstream Western eReaders, it's not really the case anymore.

Wacom touchscreen or pen input? I don't know of any eReaders that have pen input.

Also, are these devices properly GPL compliant?

They do have Wacom pen inputs, plus a normal capacitive touchscreen, and are also compatible with third party pens.

I haven't inquired about GPL compliance.

What are some models you recommend?

I quite like my Likebook, but I have the Mars model which doesn't have a pen input.