I've never used a Kindle, since Amazon has not permitted .epub books to be loaded on Kindle devices.
E-ink: E-ink devices have a very crisp display that can be seen from any angle, even very oblique angles. They require external lighting, like a lamp or the sun--no reading with this in the dark. Relative to other displays, e-ink is very friendly to batteries, and e-ink devices have the longest battery life of any e-reader device.
I purchased Nook Simple Touch devices for relatives for Christmas. The Simple Touch is an e-ink device, and I think it's great. If I ever lose or break my iPad, I'll get a Simple Touch right away.
We got a Nook Color for my daughter for Christmas. This one is not e-ink, but uses standard display technology, like the iPad. It's got a color display (I'll bet you guessed that from the name), and it runs on a locked-down Android operating system. This means you can download some apps available in the Android market, but not nearly all of them. It has a competent web browser, and with a 16GB microsd card inserted, it had no problems at all holding about 3500 books. Both Nooks (and the Nook Tablet, too) are good with dictionary/web lookups, highlighting text, etc. The Nook Color has what I'll call Book Priority. Much the same way most DSLR cameras have "shooting priority", whereby you can be looking at pictures or settings or anything, and a half-press of the shutter will immediately take you to picture-taking mode. In the same fashion, the Nook Color has a small book icon in the lower left corner. Whatever you're doing, whatever app you're in, pressing this icon will take you to your current spot in your current book. This is a nice feature.
The only real problem I've seen with either Nook model is in browsing a large book library. If you know what you're looking for, you can easily search for "hemingway" or for "11/22/63" or whatever. But if you want to browse, I believe the Nook shows 8 or 10 titles per page. The iPad, when set to list mode instead of bookshelf mode, will show a lot more titles per page. This isn't a huge deal--in practice, I just printed a 74-page pdf showing all the book titles--call it offline browsing.
I agree that the iPad can get a little heavy for in-bed reading, but I just do it anyway. By the way, I also love the night mode available in iBooks with a recent upgrade.
By the way, if anyone else has a large ebook library to maintain, or if you need to convert from one ebook format to another, I'd highly recommend the freeware program Calibre.
Also, if you want to convert ebooks from mobi, lit, prc, pdf, etc--to another format, here's a great, free, online utility that permits you to convert 5 books at a time (Calibre will do conversions also):
http://www.2epub.com/
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