I was undecided between the Nook and the Kindle like you. I got the chance to play with them both beforehand. The Nook felt 'cheap' and the screen bezel didn't feel solidly secure. The page turning took forever. The navigation of the colored LCD screen was buggy and didn't move smoothly and would freeze at times. The Kindle just feels like a better constructed device. And it is on it's 2nd generation. Therefore bugs and other glitches have been worked out and upgraded from the 1st gen model.
I also didn't like the fact the Nook was thicker and heavier than the Kindle. I also read during my research that the Nook's battery life is much shorter because of the extra power needed to run the color LCD screen.
I also trust Amazon's longevity as a viable business more than B&N. I have read that there are ways to get library books onto a Kindle but requires some research since it cannot be discussed here.