I've found my Kindle is far more dependable than my NC, (it's really glitchy), and for me personally I can read easier and longer on my Kindle (I eat books for breakfast lunch and dinner with that thing!). I haven't been able to finish a book on my NC, but I do love it for magazines! It sounds like you have similar issues as I do since you said it bothers your eyes a little, that wont go away, unfortunately. The kindle does seem limited when you compare it to the NookColor, but you need to know what you really expect in the device.
I havent rooted my NC yet, simply because I don't know what the point of having it be able to go on the internet when I can only do it in Wifi areas. I'm not out by myself in enough locations (airport? Coffeshops?) that having a tablet device with wifi only would be convenient, and I have my laptop at home. I also haven't figured out what exactly a rooted NC can do that my non-rooted can't, though, so I may be missing something big.