Lighting issues:I've previously mentioned in another thread about the lighting problems. Basically it's just a point light which is positioned in the center of the vortex. This creates a problem for the ships entering/exiting the vortex since that type of light isn't well suited for lighting objects like that. Also, the light ends up inside the model as it's moving through the vortex and thus kills the lighting effect on that ship. Ships that are further away get much better lighting that the ship that controls the vortex.
I have a plan to try and address that though. I'm going to change it from a point light to a tube light, where the light is basically spewing out from the vortex in a cone (ie, a flashlight). The source of the light will also be pushed back behind the vortex, so that it can give better lighting to the ship all the way through the vortex. This isn't really a difficult set of changes, but it's going to take a bit of tweaking, and that requires time. It's basically just too minor of an effect to spend the required time on right now. But I'll probably make the necessary changes after 3.6.10 is released in a couple of months.
Clipping issues:Known, but there really isn't anything we can do about without volumetric fogging. But fogging messes up texture rendering (which is why you don't get spec maps or env maps in fullneb missions), so it's a dead issue either way. After I get the time to finish the shader code then we will be able to handle fogging properly, without messing up texture rendering. We can take a look at volumetric fog at that point to try and make this look better. But, obviously, we'll have shaders at that point and I wouldn't be surprised if someone came up with a shader which gives an ever better effect.
(EDIT: hit the wrong button.

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Texture issues:The warpmap is one of those few effects that sort of needs to be 1024x1024. It would be a memory hog, at 4 times the memory requirement of the 512x512 version, but it would look better. At 1024x1024, and using the correct nvdxt settings, the blockiness isn't nearly as bad as it is with the 512x512 version.