Man you entered with all the glory in the new marketing trap made by Nikon. ISO and Megapixel has NOTHING to do with good pictures. 99% of the pictures will be only watched on the computer display. And on that a 3 Mpixel camera or 30 MP are no difference. It is absurd to watch your pictures at 300 % and look for the pixels and noise. Just look at them as a whole.
Sorry, but I don't buy this.
First of all, I already said that the difference between 12MP and 16MP would be minimal (and would only really matter to those who make very large prints or heavily crop their images).
Secondly, I honestly don't know how you can say ISO has nothing to do with image quality, especially for someone like me who doesn't do many B&W shots. I don't have to blow up my pictures to see noise, at ISO800 on my D90 I can already see visible noise in the image on my rear LCD screen, and I quite often find I have to bump it up to that level in slightly dim lighting conditions. I've also taken some test shots with a D7000 and the noise performance on that camera at ISO6400 is the same as my D90 at ISO1600. For me, having an extra two stops of usable ISO range is a huge benefit, even if I don't use it that often. If you only ever shoot at ISO400 or below then you could argue it's not worth the price difference, but I don't know anyone who has never had to ramp up their ISO at some point, and then you still have the other points to consider.
Thirdly, if you read my post you would have seen that I recommended to wait until the price of the D5100 drops post-launch to become more comparable to the D5000, and more affordable for first time DSLR owners. Even if it only drops to 100 Euro more than the D5000, it's still a far better camera overall so the decision would be easy in my mind.