Hop in my animated water textures package and get texture tx_wateranim04.tga. This is a flowing water texture, and also uses an alpha channel. Now try to apply it to the skybox and see if it flows. (Don't forget the txi)
As for shape, maybe another shape you might use with flowing textures (if they work) is a pill cylinder. You might be able to do a star field simulation using the cylinder, making it seem like the planet you were on was moving in a certain direction through space, at high velocity. A world with a purpose.
For a very wide and planar world (rather than sphere), you might also try this shape of skybox:
It has less wrapping/stretching issues than a sphere, and you can simulate a really far away horizon on a near-completely flat world, like say the Fugue, or an Air world. By having no surround faces, you can supply just the ground and sky textures to each saucer. There are no mountains in the distance.
Trying to open up the skybox options to non-earth worlds.
Edit: Sorry I forgot to say what that shape is. I took a cylinder with 36 faces around, and three sections high, and then I took the top corners and the bottom corners and welded them to the middle vertices. So it is a 36 face per half, double saucer shape.
Edit Again:
Using the shape above, fit to just under 84000 wide and long, with 4 tiles of texture wide and long (in the uvw mapping), using planar mapping on the Z-axis, this is what you get: a very fast flowing cloud system, like as if the planet's atmosphere was being blown away.
So yeah, animated textures using txi do work on skyboxes just fine. Granted, on my machine, it does cause a slight quantity of lag.
Also, I noticed if you go out past 100000 cm from your standing point, the skybox is clipped away, so don't do that. Make your skybox 40-80 meters wide.
I also misspoke when I said that the animwater04 had transparency. It does not. I cloned it from Torchlight 2 without the transparency layer. In my water mods, I use only the alpha setting on the mesh the texture is applied to. So I don't know yet if I can force transparency in skyboxes. If we can, then I can clone those two layer skyboxes they used in Quake and Doom.
Final Edit:
Mesh alpha does not work.
Mesh diffuse and ambient do not work.
Texture alpha does not work.
TXI blending additive does not work.
Assuming no blending at all is done on skyboxes, ever.
Haven't tried bumpreplacementtexture command yet. It may kickstart the blending process. But I find in the case of character weapons, it does not, so it probably wont.