If this can help, here is what I did to solve the problem (The launcher did nothing new to HW2 when I first used it) :
First, I moved the wca.rar in the "Data" folder.
Then, I created a shortcut for HW2
In this shortcut, I changed the "Target" :
"C:\Program Files\Sierra\Homeworld2\Bin\Release\Homeworld2.exe" -mod wca.rar
Now it works perfectly.
End of technical part.
@czacen : absolutely fantastic. Even if this is a pre-beta (alpha ?), it is beyond my wildest dreams about a WC mod for HW2 : musics, voices, ships, everything is already perfect.
Continue, it's really a great job.
@everyone else : If you haven't tested it, try the main campaign with the mod, from the second (or more) mission : Your Hiigara's Pride will be able to build Confed ships (everything except the cruiser), and the Hgn research will be replaced by Confed ones. So, let kick some Vaygr *** with your brand-new Excaliburs and Longbows !!