The K3 has 4 weeks of battery life (I got it in September and have charged it only once). And I am betting that you'll be able to get used to the black flash. It's so fast, I can't even notice it.
I have an LCD screen gadget (the iPad) and a HUGE negative is that I can't read in sunlight. Or any light for that matter. Even if I dim the lights, I can see my reflection in the screen and it gives me a headache. I'm not sure how different the Nook Color will be from the iPad (in terms of screen/resolution), but I'm guessing that the experience will be similar.
My dad loves the iPad because he can read in the dark, but I've tried reading the backlit screen in the dark and it's very tiring for my eyes. I have a clip on light ($5) for my K3 and it's really comfortable and convenient. I read during night a lot and it's perfect. If you buy a suitable clip on light for the K3, you can get over the "can't read in the dark" hurdle
I agree with tbeltrans in that the Nook Color seems to be a different "animal" (and I also repeat the question: Do you reallyyy want to read on an LCD screen for long periods of time?
). In the end, it all depends on what features you are looking for. For me, I wanted a dedicated eReader that had 3G/WiFi support (so I can email it PDF files etc). I also wanted something that truly looked like paper, so the K3 was the best choice for me.
EDIT: Also, you'll want to make sure that the Nook Color is at a comfortable weight to hold. When I read during night, I lay on my back and hold the K3 with my hands. I've tried it with the iPad and put it down immediately since it destroyed my confidence in my wrist muscles :P