For example, I'm bound to a specific PDF reader that has a very powerful annotations system. The last time I checked Epub readers, there was nothing that satisfied my requirements.
A couple of additional notes:
- the downside of reflowing is that you may not be able to take annotations that require absolute positioning
- for almost all the PDF books I've read (books; magazines are a different story, but that won't work with Epub anyway), a 3:2 10" tablet is enough; if the text is not large enough, good PDF readers can mass-crop the pages. Of course, there are ugly exceptions - books that have a different text positioning on odd and even pages (I hate them).
I don't imply it's best suited for everybody, that's the reason why I didn't specify the name.
To my knowledge there is no tool that does both. Nor, better, that also includes the purchase and download steps at Amazon.
I personally have automation for all 3 individually but have not wired them together. I think there is a nice little business awaiting someone who does that.