First of all, respect for your work!! There are a lot of great ideas pumped into this mod.
A quick game revealed that when you get the Alien ("Hulk") Ship, it remains dorment in battles. When i battled the Corrupt, they overpowered me and only the Alien Ship was left. When i clicked on it, the game just exited (crashed) to the desktop.
The balance between you and the enemy is indeed something that needs work.... The only time i was defeated was that last time by the Corrupt when they appeared with 6 (yes, SIX!!!
) of those large configurations. Great when they split up in many little ships!!
Again, it's a fun mod to play and i warmly recommend this to everyone.