In general, what I'm dong with textures to maximize their compatibility with the new shaders is removing the artificial shading and specular highlights that have traditionally been applied to make upper surfaces and things that bump out lighter, and lower / recessed surfaces darker. This allows the shaders to provide this information appropriately as the aircraft maneuvers in 3D space relative to the light source. Without this you can end up with visual conflicts where the dynamic logic of light / dark areas is being neutralized by the underlying texture. The side effect of this approach is that without the new shaders, the revised textures will look less like they are in a 3D environment with directional lighting since it is not being provided by the texture any longer.
For buildings, ships, and ground vehicles the traditional texturing method is still appropriate since they don't roll and loop. Even here the degree of shaping through brightness changes could still be reduced somewhat to avoid the shaders from over-exaggerating the effect.
The other thing I'm doing is tuning the _r.dds and _s.dds to the correct range of grey shades to produce the appropriate response to the shaders. Some of the older shading and reflectivity files produce too much glossiness now at the levels of brightness they were originally drawn with.