It's definitely a matter of personal preference and habits. My boyfriend and I have a Kindle and a Nook, respectively. He loves his Kindle, and he does most of his book buying from Amazon. He's not very computer-savvy, so he doesn't know about the lack of .epub support -- but I don't think he cares, either. He likes the keyboard and the look and feel it; he also loves the magazine subscriptions for the Kindle.
I like my Nook because we live right near a B&N store. I buy truckloads from them, have a membership, etc. It would be a definite drawback for me to have a Kindle, because I couldn't read B&N books on it. Also, if you want to buy outside Amazon, your buying choices are more limited (not all that much, but a bit) -- unless the ebook store carries the .mobi format and/or you know how to convert things. I also check out tons of library books, so... It just fits me better, personally.
Both are great e-readers, in different ways. It just depends on which one fits your style better.
