Not bad Stu.
You might want to work on the lightning, perhaps take it out of the field of view completely. One way that could look good, but wouldn't be antirely Freespace correct was to do the lightning inside the distant cloud banks. That way, there would be bright flashes, etc, but no jagged lighting bolts visible.
Something else you might want to take into consideration is moving your camera back a bit, making it stationary and opening its FOV some. Especially in the sequence where the missiles are streaking toward their target, it begins to feel quite claustrophobic. By pulling the camera back and having it pan from a stationary position, the movement of the missiles becomes much more dynamic. If you can keep the missiles just to the right of the center of the screen, it will also add ot the illusion of speed.
Speed is my next point. The whole sequence felt kind of slow to me, like I was watching a slow motion replay of the whole scene. If you've got your rendering done at 15fps, try 30fps and see how that looks.
On the chase sequence, again, I have to say pull that camera back and open the FOV a bit. An0n nailed that one on the head. Right now, you're so close, and so tight, it feels really confused, and we don't have a real sense of what's going on.
Finally, what program are you using, and does it support an overdraw area? In lightwave, I can specify how big each frame is AND how much of that frame is actually within the camera's FOV. The overdraw allows for effects to start and take place outside of the FOV of the camera, which prevents some of the wierd edge-of-screen effects like you see on the terran beams as you pan the camera toward the shivan ships.
Most important, though, nice damn job. You did far better than I could have done, I think.