Honestly, after reading your criteria, I'd suggest you go with the Sony. And this is coming from someone who loves the nook.
The reason is that it sounds to me like that's what you really would rather get her. I don't think refresh rates are a problem on the new ones, and you already said that wifi is not a deal breaker. So, the only reason I see for you not to get one would be the price, if it's too expensive for you.
If price is too much of an issue, then I would recommend the nook. The battery life really isn't that big of a deal. The collections/folders thing may be addressed in a future software update; B&N has been very good about their updates.
And the Kobo, well, I don't see anything special about it, but really, any of the three are fine choices.
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