Capacitive is just a far superior touchscreen technology. It is faster, it is more more precise, it supports multitouch gestures (zooming or rotating)... But as GeoffR says it has also some drawbacks.
So I cannot imagine using a smartphone without capacitive touchscreen. But within an e-ink Reader I also prefer maximum image and contrast quality rather than a "better" (even with some disadvantages) touch response. IR is just good enough unless you really intend to make a serious use of the WebBrowser...
Having said this, there are IRs and IRs. Although Kobo Aura HD and H2O work, they are far worse than PRS-650 one. As I have said in other threads, Kobo IR is just quite less precise and it just doesn't see the Sony stylus (while PRS-650 obviously does...)
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