I must say that many parts of the scenario look strangely familiar (and I don't mean it reminds me of Homeworld).
Overall not bad for a first scenario, unit graphics are nice and the music is impressive but...some quick questions and observations from playing a couple of rounds.
If Kharak is destroyed, why is it still there? Get rid of it with a terrain change event after a few turns of warning. As settlers are carried on the mothership, i think the game will continue on.
My ships can easily go all the way to Hiigara which is so near. Why not put Kharak and Hiigara at opposite ends and force the player to go through the necessary stages in the right sequence?
To be even vaguely true to Homeworld, you shouldn't know how to build all the different ships from the beginning. (i.e. why no research?) Besides, it makes it too complicated at the beginning.
The intro panel is too tall and goes off my screen, maybe you should make it wider but shorter?
Notice that the resource controller has become a troop carrier? Why not make the assault frigate a transport with attack and defense factors. As the AI never plays the human race, it shouldn't be a problem.
resource controllers can be given the sub flag if you give the collectors the helicopter + missile flags.
As for the overall unit look, try a function called 'sharpen' available in all photo editors (including the microsoft one that comes with windows)