Let's look at some of the heroes:
Bold Captain (BC): This seems a little overpowered, and not necessarily in the theme of a "bold captain." Effectively it lets you duplicate the power of any friendly hero on the ship you are on - so you can BC an SA to get two sets of bonus action points, or BC a saboteur to get two chances to sabotage an enemy ship - the best strategy is often not to be a "captain" and just go on an enemy ship to help heroes out there. A good strategy for the Federation (since they're the only faction that gets BC as a favored class) is, let's say if they get 4 hero points, to get two BCs and an SA, put them all on the same ship, and get three activations of the SA ability per round (instead of two if he just got two SAs).
Seasoned Admiral (SA): This seems like a not very well designed ability. Not because it's overpowered or underpowered, but because it's basically "free" APs every round - you don't have to do anything special to use it. Most of the other heroes' abilities you have to get the guy on the ship you want to use it on, and that takes time and resources, and risks putting them in harm's way. The SA can use his ability from anywhere, so if I were the Colonials, say, I could put my SA on a CSV, send it way away from the battlefield to protect it, and he'll still be just as useful as before. Also, do the bonus APs stack (say if you BC him, or have two SAs, and use the two activations on the same ship?)
Legendary Engineer (LE): You still haven't made clear how many hit points the LE's free repair roll is worth. Also it might be a good idea to allow the free repair roll to be a free saving throw instead (that way the LE can try to repair a system that's been reduced to zero HP).
Indomitable Leader (IL): Can he destroy enemy boarding parties even if there's no friendly combat units on the ship, just him? If so a useful tactic might be to put him on an enemy ship, slowly whittle away their combat units (and the only way to kill him is with a Bounty Hunter) and then after they're all destroyed, bring a friendly combat unit in to capture the ship.
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Also, another potential problem I see is that the only heroes that can get rid of other Heroes are the Dark Lord and Bounty Hunter, and only two of the factions even have access to those Heroes. So if you're fighting another faction you can get as many Saboteurs, Spies, or ILs on board enemy ships as you want to do havoc, and there's nothing they can do about it.