I wouldn't have ended the story with the death of the boss. Maybe things would get a bit easier, but your objective is to fully secure the city, not just to kill the mutant boss.
Looking through the skill tree, I see Quake Leap.
"Oh, something that could be good if I master it, but I don't have the time."
Le think: (After being mauled to death by OP dogs.)
"Eh, maybe I can use it to escape."
Le buy. Le use.
"OH MY GOD DEATH BODYSLAMS W/ NOCKDOWN FOR EVERYONE!"
An excellent game, the side missions were a nice, refreshing pwnage. Maybe you could have obtained a bounty from destroying ships or had a Tech and leveling option, though this goes against the game's basis.
Secondary ammunition needed, maybe you could expand on the guy's abilities a little more, maybe with level ups. That aside, the physics engine made this game a cut above the rest. Enemy dialogue might help as well. Good play style and easy adoption.
This is a solid Command and Conquer tribute with it's own little things. For people who like long game strategy, but not that general. However, the password thing is a bit of a FAIL.