You can't compare noise when one is 12 MP and the other one is 25 MP.
Yes you can, and should. What do you think happens when you print? That's right, your 12 MP image is going to print into the same area as the 25 MP image. This doesn't just apply to print, but also to web publishing. Let's face it, you're not going to publish an image at 12 or 25 MP on the web and then let force your customers to view them at 100%, right? Your 12 or 25 MP file is going to get resized down to 600x400 or something for display in a webpage.
It will be closer than what you think if viewed at equal resolution, at least till ISO 1600 and maybe even 3200. At ISO 400 and lower, A900's 25 MP photo will have far more detail than D3. As I said, it will beat the crap out of D3 at low ISO.
The D3 and A900 target different markets. If the A900 didn't do well at low ISO speeds, then it's failed at it's job. Similarly the D3 is targeted at high ISO high fps shooting, where MP count doesn't really matter.