There are probably many of us that are seeing this since Barnes & Noble announced NOOKcolor, which is people clamoring to get it and saying Kindle is behind the times. A huge fact they are missing, and that Barnes & Noble is conveniently hiding under the table, is that the screen is no longer E-Ink. Being back-light it is more than likely simply an LCD screen. There is where the problem comes in and in the rush to have "the best gadget" people need to be aware of. The number one reason some many move to E-Ink in the first place is how much less eye strain it causes.
From simple personal experience I can say that when I have the time I can read for hours on end with needing to "rest my eyes" or getting tension headaches that same amount of reading done on an LCD would cause. To most that have tried eReaders the difference can be felt almost immediately when moving for looking at the LCD screen on their desk to going to their favorite eReader. It truly is like reading a book and while it is inconvenient to not have the back-light at times that back-light it part of the problem. That is the thing while in the title I might say Kindle vs. NOOKcolor this is more about E-Ink vs. LCD. If you really like nook better then buy it, but buy the E-Ink version while it is still available. Your eye will truly thank you for the difference.
Since I know I might not be the most persuasive voice out there here are two very good links that might help you understand all of this a little better. First is Amazon's explanation of E-Ink which can be found half way down on their Kindle product page titled "E-Ink 101: Compare Kindle's Screen to Traditional LCDs". The second is a microscopic comparison of E-Ink and LCD(http://www.bit-101.com/blog/?p=2722).