I made the entire thing, from beggining to end, in FRED.
If you want the mission, I can provide that as well, so you can fiddle around with it.
To address some of the points you mentioned:
2.
There's some really good scenes in your video, however, theres some rather nasty things in there too:
a) The messy white beams that seem to stay solid forever - they look like some odd lines
An experimental beam, the NBeam (one of my creations). That can be changed now that I have an nice new texture

b) the close up of the thruster effects when the capital ship jumps out
huh? Timing issue, no worry about that.
c) the 3D shockwave is just ugly
What 3D shockwave? where?
d) The odd textures on the Hecate
Again, my fault. Those are my experimental textures.....rather ugly, I know lol

e) The framerate is a bit low
An issue with my PC mostly. This is fixed however, with Kazan's new build with the time compression

f) You use the stock sun, which looks a bit low res
Not much of a problem. I can use the new suns out, if I can find the proper thread...
g) The shot on the hangar - i would rather stick the camara inside the fighterbay, so you see the ships leave from behind you - they look a bit odd coming out of that 'black line' (as the fighterbay shows from this perspective)
hmmmmmm.........interesting....i'll try it...
3. If you could fix the issues mentioned in 2. this probably would be the most amazing FS2-related movie I have ever seen. Please, try to fix them (or explain us how you made it :-) ) - *this* is the kind of publicity the SCP needs to grow and expand.
Hmm.....sorry, I cant work on this, since im working on something similar elsewhere.
Edit: never mind. Im going to try running this again with some of the suggestions given so far. With the new Kazan build, i'll see if i cant get some better framerates..