For the animated humans I intend to support skeletal animation.
For those of you that don't know, it's an animation technique that uses bones and bone weights to animate 3D meshes. It's a standard technique and well documented.
I also intend to use proper animation blending, so they will look good and you can do special case animations of you so wish.
3D craters are done with texture splatting. Basically in the terrain vertex generation you detect the vertex is within a crater (point-sphere collision) and mix the vertex height with the height of the crater. It's a fairly cheap process but produces very good results. You can even have overlapping craters and it works.(The number of overlaps is limited though).
3D waves are a no brainer. I use a FFT based solution.
Atmospheric effects will come later, but the volumetric cloud system I use can easily adapted to dust storms.
My atmospheric model is very complex, I chose to do a full simulation because I wanted to be able to model icing and contrails in a realistic way.
Debris will be handled as collidable objects, actually to simplify the code they are flak particles with different physics.
Forests will be handled as a two stage system. At a long distance they will be volume textures (very similar to the cloud code). At close range they will be handled as full 3D meshes rendered as instances ( a trick to speed up rendering large numbers of 3D models which only vary by shader variables. They have the same vertices and textures, but can have different colours and orientations)
Rivers are going to take some work, but that's for later.