Totally awesome mod, I've really been enjoying it.
But I do have a few suggestions,
1: Make missiles able to travell through water (maybe lava also), I really want to build an underwater missile submarine or something, or a volcano base with missiles firing out the middle ect. I think it'd be really cool.
2: Make either Radar's or Missile Defence Systems output a redstone current when a missile is detected. This would just allow for some extra cool things, like blast doors closing, or makeing alarms sound ect. Once again I just think it'd be cool, and hopefully not to hard to do.
3: Make Missile Targeting Systems fire their attached missiles when a redstone pulse is applied. This could be used for traps, or something like that, picture it somebody snooping around your place, launch a missile right at him!
4: Allow Superconductor to be covered in CF. This is just so using it is better, it shouldn't be to hard to do, should it?
5: Fix the re-entering missile and passenger module textures. I know this has probably been said a lot, but hey...
6: Fix the destruction of missiles by other missiles crahing the game. Not sure if this one is just me, but still...
7: Add support for SMP. I know every man and his dog has said this one, but hey, repetition is good right? 
8: Fix the parachute. Once again this might just be me, but it doesn't seem to work...
That's about it for now. Just my thought on how to make this fantastic mod better.
Regards, The_Marksta
P.S. Does Kentington work on this anymore/read the thread?