When I first set out to buy an e-reader, it was mainly to read and annotate pdfs, but I soon realised that no e-ink reader would provide me with the functionality I needed. In the end, I got an iPad for that purpose, which I use with the iAnnotate app to mark up my pdfs. If you are going to spend a lot of time reading and marking up pdfs, I'd strongly recommend looking into second hand tablets - you could then install the kindle app and still read all your Amazon books on the same device.
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