I've read through the rules and it seems like there are a few things that need clearing up:
1 - Where are the breakpoints for things that happen "per round"? For example, an aura damages all the ships in it once "per round" - when in the round does that happen? And shields protect against a certain amount of damage "per round" - when is the beginning and the end of the round in that case? Probably the easiest thing to do for shields is to make a round be from the shielded ship's turn to the next ship's turn. That way shields basically work like temporary HP in D+D, and whenever the player activates their shields they set their "temp HP" to the shield level.
In general I would suggest rewording everything that requires you to spend APs "each round" to just be spend the APs to get an effect that lasts until the start of the ship's next turn. That way there is no confusion.
2 - Am I correct to assume that you can only activate each ship system once per turn?
3 - Can two or more ships occupy the same hex? If they end up in the same hex (say because a ship gets crippled and can't thrust, and its speed moves it into the same hex as another ship) what happens?
4 - I don't see much reason for ships to form up into squadrons. It seems like it makes them strictly less powerful offensively - if they each fire individually they can do their full damage per shot (usually around 1d4 per fighter) while if they are squadroned they will do at most 1 damage per fighter per shot. Just about the only reason to squadron up would be to protect against auras and other AoEs (because they would only get hit once).
5 - You say that in a boarding action, a ship is captured once "one force" is defeated. I assume you mean the ship is captured when the "defending force" is defeated.
6 - What's an "area burst"?
7 - If the Bold Captain moves from ship to ship, does that affect the initiative order? (This also applies to if the Seasoned Admiral is killed or switches sides.)
8 - Is it possible to heal defending forces during or after boarding actions?
9 - What does "capacity 6" mean on transporters?
10 - Does the Saboteur have to be on the ship it is sabotaging?
11 - When it says ships can defend with "combat forces detailed in its stat block" that means forces that are listed as forces that it can send to board other ships with, right? (I can't find any examples of other combat forces that are listed in stat blocks.)
12 - As written the laser tower will never be able to use its repair ability, because as soon as it gets knocked down to 2 or less hit points it will be at zero AP (because 25% less than 1 is 0.75, rounded down is 0). This is probably also an issue with other craft that have 1 AP - probably you want to say that the number of AP per turn can never be less than 1.
13 - What's a "Raptor" (Colonial Battleship power)?
14 - The Colonial Support Vessel's "8 marines" - are the stats per marine? Same question for the Spartan Scout's boarders.
15 - If a ship's shields have been activated this round, but all its damage absorption has been used up, does it still count as "shielded" for the purpose of effects such as the Alliance Warship's Neutron weapon?
16 - How do you know whether a weapon is an "energy weapon" for purposes of the Shadow Battle Spider's ability?
17 - Can a ship with a boarding power send boarding forces over to a friendly ship to help that friendly ship fight off enemy boarders? (In general what happens if there are more than two groups of forces on one ship - I assume each group decides which other group to attack.)
1 - Where are the breakpoints for things that happen "per round"? For example, an aura damages all the ships in it once "per round" - when in the round does that happen? And shields protect against a certain amount of damage "per round" - when is the beginning and the end of the round in that case? Probably the easiest thing to do for shields is to make a round be from the shielded ship's turn to the next ship's turn. That way shields basically work like temporary HP in D+D, and whenever the player activates their shields they set their "temp HP" to the shield level.
In general I would suggest rewording everything that requires you to spend APs "each round" to just be spend the APs to get an effect that lasts until the start of the ship's next turn. That way there is no confusion.
2 - Am I correct to assume that you can only activate each ship system once per turn?
3 - Can two or more ships occupy the same hex? If they end up in the same hex (say because a ship gets crippled and can't thrust, and its speed moves it into the same hex as another ship) what happens?
4 - I don't see much reason for ships to form up into squadrons. It seems like it makes them strictly less powerful offensively - if they each fire individually they can do their full damage per shot (usually around 1d4 per fighter) while if they are squadroned they will do at most 1 damage per fighter per shot. Just about the only reason to squadron up would be to protect against auras and other AoEs (because they would only get hit once).
5 - You say that in a boarding action, a ship is captured once "one force" is defeated. I assume you mean the ship is captured when the "defending force" is defeated.
6 - What's an "area burst"?
7 - If the Bold Captain moves from ship to ship, does that affect the initiative order? (This also applies to if the Seasoned Admiral is killed or switches sides.)
8 - Is it possible to heal defending forces during or after boarding actions?
9 - What does "capacity 6" mean on transporters?
10 - Does the Saboteur have to be on the ship it is sabotaging?
11 - When it says ships can defend with "combat forces detailed in its stat block" that means forces that are listed as forces that it can send to board other ships with, right? (I can't find any examples of other combat forces that are listed in stat blocks.)
12 - As written the laser tower will never be able to use its repair ability, because as soon as it gets knocked down to 2 or less hit points it will be at zero AP (because 25% less than 1 is 0.75, rounded down is 0). This is probably also an issue with other craft that have 1 AP - probably you want to say that the number of AP per turn can never be less than 1.
13 - What's a "Raptor" (Colonial Battleship power)?
14 - The Colonial Support Vessel's "8 marines" - are the stats per marine? Same question for the Spartan Scout's boarders.
15 - If a ship's shields have been activated this round, but all its damage absorption has been used up, does it still count as "shielded" for the purpose of effects such as the Alliance Warship's Neutron weapon?
16 - How do you know whether a weapon is an "energy weapon" for purposes of the Shadow Battle Spider's ability?
17 - Can a ship with a boarding power send boarding forces over to a friendly ship to help that friendly ship fight off enemy boarders? (In general what happens if there are more than two groups of forces on one ship - I assume each group decides which other group to attack.)