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I went from reading on Sonys (PRS-350 and PRS-650) to a Kindle Paperwhite 2 and then to a Kobo Aura HD. Honestly, I don't find much difference between the responsiveness of the capacitive and IR touchscreens.
Both the IR touch screen of the Sonys and the capacitive screen of the Kindle work well for me. That being said, I don't use the highlighting feature, or access a lot of footnotes. I do use the dictionary lookup quite a bit and it works well on all my devices.
You asked specifically about the difference between the IR on the Sonys and the IR on the Kobo--I don't notice any difference in responsiveness or accuracy. Once in a great while, my Aura HD does not respond to page turns--taking a couple taps to turn the page. But when this start happening, a reset of the device clears it right up. This isn't a frequent problem--probably only happened twice in the eight months I've had my Aura HD.
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