Amazon's Kindle is excellent. It's note-taking system and export are great. But only limitation is, they will only let you get highlights for the books you bought from Amazon.
If you get books from free sites/other providers, if you read PDFs, research papers, Amazon will not let you get those highlights out of kindle in their application.
There is also a limit to how much you can export from books you bought from them. This is ridiculous and stuff like that is what makes owning an ebook to be not as same as the physical copy. I hacked this together within an hour, so highlight and export to your heart's content.
Built by Vignesh