My thoughts so far.

Thanks for the feedback! I will try to improve it with time and add some new items.

Some notes:

[*] The ships clip into each other due to the drawing order of sprites. I did not have time to create my own drawing order for the game engine, so when the ships are pieced together from many pieces, and the turrets are on their own layer, they clip when they are on top of each other.
[*]Units firing when exploding is up for interpretation. I think even in this real world a big naval ship carrier or such can keep shooting even if it's about to explode to pieces.
[*]"Harvester" - units can harvest resources from nearby exploding ships. I think this is what you mean with the station that costs a lot but seems to be weaker. Granted I could have tried to get a better explanation somewhere but I only have it in the help menu now.
[*]I have added BSE Marineclone to make replenishing marines possible.

Thanks again for the feedback!

[*]

 on the drawing order it seems like the solution would be to have the program draw each individual ship then that ships turrets then the next ship and then the next ships turds and so the layers wouldn't intersect in the render calls. as far as the late firing goes when an expanding cloud of vapor and debris is still hurling missiles lasers and projectiles at my ships its firing well after the vessel is dead. cool tips of some kind might help with understanding what the Harvester station and is and the Marine clone ship especially considering that you sometimes use Whimsical names for these things but it's nice to know they're actually there and have a purpose. it might also be useful to consider adding the Marine replacement ability to the Starbase repair beam as a secondary means of replacing Marines. repairing space stations probably should include a limited slow self-repair simply because the space station is going to have more of an ability to self repair than a spaceship it wouldn't necessarily need to be anything fast. but it would go a long way towards dealing with some of the headaches especially those points where you upgrade the whole strength but then you have to turn around and spend money to get the upgraded hollow-points. considering that space stations generally have to be more self-reliant they can't exactly put into port I think this is probably something that should at least be considered. as far as limiting the number of Marines I disagree with doing that purely because this is not a singular engagement taking place over the space of a few hours but it is instead a sector Invasion which I would considered to be scaled so that minutes equal hours or days or weeks therefore it's logical to assume that additional replacement Marines would become available overtime and not unreasonable to assume that you would be able to distribute them amongst those ships conducting boarding operations are fending off boarding operations. the pace of the game means that if replacement takes a considerable amount of time the ability becomes far less useful and remains a novelty. the speed of replacement should scale with the pace of combat. so is not to interrupt the immersion in the experience. overall I think that many of these abilities that you have tied up in specific ships and stations would have better fit the game if they had been modular like the weapons instead. Available station and ship resources simply aren't large enough to support specialized one off single ability space frames. the end result is that the vast majority of players we'll go for the real fire power over the specialist ships and me personally I have yet to actually be able to work through the entire research tree to get to the specialist ships before I've pushed the Hostile forces over the resource Tipping Point to where they're no longer capable of meaningful offencive action. this means by the time I'm actually in Striking Distance research wise of any of these specialist ships the enemy's resistance is already collapsing and I simply don't need them to win. making them unlockable I think if they're not going to be made into modular components is probably the only way the players are going to be able to use them early enough in the game for them to serve their intended purpose. on a side note is there any way you guys could fix the harbinger class ship? I mean we all know the things based on a colonial Battlestar. it's got the hangar Bays but it needs the heavy weapons and point defenses to go with it. that ship should be on par with the seeds battleship and it's not. it's not nearly Tough Enough and not nearly heavily enough armed I'm just saying.

oh and quick edit if you do make Marines far more available then the AI at least it normal and legendary levels needs to make much more aggressive use of it. right now it seems like only reinforcement fleets not those built-in sector ever have access to Marine transports and really these transports are only effective at boarding stations because the stations right now lack the point defense to effectively shoot them down most ships especially if they're running away can gun down Marine transports with ease.