Basically, your officer's training level has a HUGE impact on how often they can use their abilities. With the rate at which the game gives us expertise points, it will be level 8 or 9 before you have enough points to fully train your officers.
Life would be easier for the newbies if the story officers they got were already trained, even just halfway, in their skills. That would give new players a better feel for when and how often to use their ship's abilities versus the Gimp O Tron 9000 cooldown rates on untrained officers.
This is in fact the whole issue with low level content. You have too few abillities and they take too long for a cool down. Sometimes the succes of a mission is only a matter of luck, having a lot of hits and some crits, since you can only pew, pew pew.
Another problem with Boffs at starting level is the fact that you don't have enough money to retrain them. There are just a couple of skills useful at starting level, tac team, E power to shields are among them.
So when is the game the most challenging? First level on your first character.