To make the heroes more interesting, one thing you could do is to, rather than just give each hero a passive benefit, also give them active abilities. But rather than have these be separate things a hero can do on their turn, they're abilities that the hero grants to the ship. And these abilities are things that cost something to use or require tactics that aren't normally used, so you have to decide whether and when to use them. Borrowing from 4e you could have an "at-will" that can be used all the time and a "encounter/daily" that you can only use once per game. (The "once per game" is by hero rather than ship, so you can't get it back just by moving from ship to ship.) For example:
Legendary Engineer:
"We Need More Power" - Once per turn, the LE's ship can spend double the normal action points on any one action to get a +4 bonus to that action.
"Overload Reactor" - Once per game, the LE's ship can use up to 10 action points over its normal allotment. At the end of the turn, it takes 1d4 damage per extra action point it used.
Science Genius:
"Subsystem Targeting" - Once per turn, when targeting a specific system on an enemy ship, the SG's ship can choose to disable it until the end of the SG's ship's next turn instead of doing damage.
"Reverse Polarity" - Once per game, after the SG's ship rolls a d20 for any ship system, it can flip the die over (so a 1 is instead treated as a 20, a 2 is treated as a 19, etc.)
Plucky Pilot:
"Shake Sensor Lock" - Once per turn, the PP's ship can spend 1 AP to roll a d20. On an 11 or higher, all sensor locks that enemies have on his ship are dropped.
"Target Weak Point" - Once per game, if the PP's ship ends his turn in the space of a Huge or larger ship, he can declare that he is going for a "weak point." On the PP's ship's next turn, if the PP's ship is in the target ship's space (or moves there) the PP's ship can spend 2 AP to make a special attack roll at a -10 penalty. If the attack succeeds, the target ship takes damage equal to 1/4 of its maximum hit points. (Note: This is intended to simulate something like the Death Star "trench run" where you fly over an enemy ship looking for a weak point.)
Squadron Leader:
"Covering Maneuver" - Once per turn, the SL's squadron can give another Medium or smaller ship within 2 hexes +2 to defense until the end of the SL's squadron's next turn.
"Attack Pattern Alpha" - Once per game, at the beginning of its turn, the SL's squadron may initiate a coordinated attack on an enemy ship system. This increases the squadron's available AP that turn to its remaining HP value, and gives it a +4 bonus to attack, but all the attacks have to be made at the same specific system on the same target.