First, I can honestly (truthfully) say that I really have no preference for e-ink vs. LCD for indoors reading under normal lighting conditions. I honestly truly don't care.
People talk about eye strain but I don't see it myself because I spend 8+ hours a day reading on an LCD screen here at work - and my job generally involves real reading... often tedious 1's and 0's. I read on LCD's the whole time except for occassional breaks. If I'm not reading, then I'm writing, which to me is pretty much the same thing as reading. I will admit to being very picky about the LCD that I use to do all these reading and writing. It took me three sets of monitors (and one very irritated IT worker who swapped them for me) before I settled on my current pair of LCD displays. But aside from being picky... I don't get headaches, and I don't believe that I get eyestrain and I really don't care which type of display that I have. I was even happy with my old 22" trinitron CRT's.
So indoors I have no preference, and I don't get eyestrain from reading on LCD's.
Outdoors, the LCD on an iPad is totally useless - the screen is too glossy and unless you concentrate all you see is the sky. So outside e-ink isn't merely better, e-ink is the only thing that works.
And then in very low light (an international flight, my bedroom), yes there are those clip on lights... but I don't like them. I don't like them with regular (paper) books, and I can't imagine that I'll like them on an e-ink reader. You can say that I'm being inconsistent or whatever, but I don't like the light from those clip on things and I never have. I like LCD's in the dark. They don't bother me, the look nice. As long as I can dial the brightness, I prefer LCD's to little clip-lights.
Still, to me this is what I like. This isn't about "the best", it's about what we want. It's like someone saying "vanilla milk shakes are the best", and for lots of people that's probably true. But if someone likes strawberry milkshakes that doesn't make them wrong. Most people prefer e-ink - I'm one of the few who don't really care and to some small extent slightly prefer LCDs. That doesn't make me wrong. Just unusual.
As far as the science discussion, I don't understand how refresh rates play into this discussion at all. LCD's don't refresh except when they change. And when you are reading text, nothing changes. If we really wanted to compare refresh rates, e-ink refresh rates are appalling - like 750ms. But they don't refresh unless you change the image, so it doesn't really matter.
I agree with Zerocool that it doesn't appear like the scientist being quoted knows what he's talking about. Even if I do agree with his conclusion.
Back to the original question, if all someone wants is an e-reader and the only choices are a Kindle and an iPad, and they aren't looking at a Kindle DX, then I think the choice is fairly obvious because of the price difference, and the answer of what's better is Kindle. If we are comparing the Kindle DX and the iPad directly, since the price and dimensions are basically the same for both, and if we are still only considering usage as an e-reader, then it comes down to LCD vs. e-ink. And if there's still no winner because someone is like me and doesn't care, then I'll award the winner of "best" to iPad because it supports more formats than Kindle and it's color.
Still if I was going to get an e-ink reader, I'd go for something cheaper and more open than a Kindle and something that has an SD slot.