The title sets the topic: "Boff's are pretty inept, just look at their never-improving ability slots for proof."
An ensign boff has 1 slot for space powers and 1 slot for ground powers. These slots are "ensign grade." As the boff increases in rank these first slots, as those that will follow, will never improve.
You may not noticed this on the ground, as Boffs can use all of their powers then. But in space the story is different; in space, no matter how hard the boff tries it will only ever be as powerful as its station allows for which means a Commander is as valuable as an Ensign if that is the only seat available for it - and this impedes the "meta-game" specific to how powers and game-play experience mingle which is a huge contributing factor to why certain powers are favored and others generally ignored.
PROPOSAL: To overcome the meta-game impedance mentioned above, turn all boff powers into "level-less" abilities which are as effective as the boffs current rank allows for and allow for those powers to be trained in whatever slot the player chooses.