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The issue is the clunkiness of the software used to make notes, annotations etc. There are several e-readers equipped with styluses for note-taking, but the design decisions the manufacturers have chosen have typically been quite frustrating for users
Example: The Boox M92. When you pull the stylus out and attempt to hand write a note on the document, it won't actually write (instead will recognise your swipe as a next or previous page action). The user must open an options menu, choose the annotations tab, then select line thickness - THEN can annotate the page.
Singling out the Boox in particular here - but the general issue is that when a manufacturer makes the design decisions for software features, the likelihood is that you're going to end up with something clunky.
This is why tablets - with the Android or Apple App stores, have well designed features. There is not one single entity making design decisions - there are thousands of app designers. If the app is badly designed, it doesn't mean people get a different tablet - they just get a different app.
This an issue with e-readers. They've only got one shot at a time to get the software right. Not saying that they won't get decent annotation in there at some point - but the better development model is probably app based in terms of features and obsolescence.
Could e-readers develop an app store? Probably not unless the screen tech improves.
Which brings up colour - e-ink triton is slow, has a poor colour range, low saturation and the colour filter makes both the white and black pixels appear greyer than they should. Nope.
Liquavista - maybe. My bet is on an electrowetting tablet in the next 5 years - app based so there is decent software for whatever features the user might be after - annotation, reference management, notetaking, book discussion etc.
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