As the game progresses, you learn to get used to the number of bridge officer abilities. It's worse in this mission though, since you're scrambling to figure out what all the powers you have are, even if you're used to flying a VA ship. The progression through the game gives you a chance to get used to the powers as you get bigger ships.
As for automating powers, may be able to do the same thing as you can with weapons, i.e. right click the activate icon so it has a green border and will continue to activate after the first use.