about the itani who has to sit at the back of the ship and power the energy foci for the ship (in accordance to celkan's interpretation of the story):

give him something to do, make him really have to concentrate on something. my favorite example of such an activity is tetris.

The itani could choose what level of tetris he wants to play at. the higher the level, the harder it is to maintain the energy foci, but the more protection you have;
if the itani is pretty good and reliable at the game, he can make the energy shield run nice and smoothly.
If the itani loses in the game, the ship he is in will lose energy focus for a moment. not good.

now replace "tetris" with any other minigame you can create on the fly.

it could be snake (with the snake staying the same length/speed throughout the game),

it could be zapping shots falling from the sky, it could be a pong-like game, with the player having a little "shield paddle" absorbing enemy-fire-pong-balls that fall down...

just give the chap something to do.

I quite agree with you, harvestmouse... but man that sounds a heck of a lot like Puzzle Pirates the way you describe.