So, like an earlier poster, I am a signal processing person. Here is my perspective on AA in audio. Perhaps some of you have some thoughts on how it applies here.
Aliasing must be avoided at all costs. Any sampling technology must have something ahead of it that limits the frequency of what it receives to half of the sampling rate. Anything else is an ERROR. If you can be absolutely sure that you will never encounter such frequencies, then fine. However, I think in photography that would be equivalent to saying that the resolution of your lens system is low enough that fine details will not appear. That seems a poor bet.
In audio we have sampling rates such as 44khz. Which means that we must never see frequencies above 22khz. The problem is that real world low pass filters have rolloff. So to be sure that 22khz is 96db down (the limit of 16bit samples) requires that frequencies such as 19khz will be somewhat pulled down as well. No one likes this. The solution to this in audio was to over sample. So you sample at 88khz. So now you have to avoid things above 44khz. A real crappy AA filter pulls things down but by the time you get to 22khz there is no rolloff at all. So you over sample, anti-alias, and then down sample to 44khz. Presto, you have great audio frequency response out to the edge of the system.
So applied to photography, it looks like this: at 12mp you use an AA filter and you lose some fine detail because AA filters have roll off. Instead, run things at 36mp (oversample) with an AA and down sample to 12mp and you have essentially perfect 12mp images. Running the 36mp system without an AA would only make sense (to me) if you KNEW that the lenses were low enough resolution that they were doing the AA for you.
So...That leads to my question(s). Are the Nikon lenses high enough resolution to exceed the resolution of the 36mp sensor? I think the answer is "yes". This I suspect because the pixels at 36mp are very similar to the grain size of film. Has Nikon or anyone else done studies or white papers on this?