It's just the aspect ratio. They'll have the same quality, since the 9mp video is just the same as the 12mp video except that parts from the top and bottom are omitted. Think of it this way: if you have a 12in tall stick, you could cut off 1.5in from the top and bottom to make it 9in. This was done to create the 16:9 wide-screen ratio. What this means is that if you use the 12mp choice, your video will have black bars on the left and right if you play it on a wide screen, basically the grey area in your picture. If you use the one with a 16:9 ratio, it will cover up the entire screen.
There's really no difference in quality whichever one you use.