The game gets repetitive after the first third. And you should add a way to re-assign upgrade points -- currently you max out at commander level 24 and don't get any more, and can't re-assign them. I beat everything except the third boss (the one in the last battle) and would like to try re-assigning points to try something else, but I can't. And I'm not going to play through all those battles again.
It's silly that the other guns don't fire unless you personally fire them. Don't they have crews or something? They should at least fire ineffectively or slowly.