I too have woundered this. My family has owned Yukons I know were flexi fuel capable, but the only E85 pump within 300 miles of here is a private government owned one.
That said, there would be several issues with running E85. First you need larger injectors because you have to burn through more E85 to get the same power and the fuel map has to be able to work on a broader range of mixtures. I think it may be a tiny bit more solvent, but most modern fuel systems are probably more than capable of workign with E85. So on a manufacturers level it wouldn't be too difficult for them to implement the necessary changes, but to us it would be a lot of reverse engineering, mainly in the computer fuel map.
It's unfortunate too, E85 is much cheaper than gas right now with all the subsidies they give it. And you get a recombant CO2 cycle with growing the corn to make the fuel. You see it a lot more in the mid east states to my understanding.
As far as CNG I think someone here a while back did some experiementing with shooting some CNG in to the intake and it seemed to run. Again, this is a fuel map issue. My family has a Ford F-150 with an aftermarket technocarb kit on it to run on LPG fuel. It's a very nice system, but requires it's own separate computer and also has features implemented to defeat the truck's computer from setting certain check engine codes. I like it though for a big truck because the fuel has been $1.59 a gallon for months and months.