1) When you update an (already uploaded) ship design to steam, it only captures the first 256 characters of the previously uploaded description. Any additional description is lost.
2) In the design screen, I think it would be more user-efficient to split the weapons into two categories, forward and flipped, rather than have them mingled in one huge list (I previously suggested just having the forward facing weapons, and pressing control click to flip the weapon).
3) I believe the game too strongly incentivises boxy, square, unappealing ship designs (aka "the flying shoebox"). One contributing factor is that (as I understand it) "a module gets a structural bonus for each cell edge of each its edges that is contiguous with another module edge". I suggest changing this to "a module gets a structural bonus for each of its edges which has at least one cell edge contiguous with another module edge".
4) The rams look like they are supposed to protrude from the ships. Which seems logical. But due to the structural bonus system, there is a kind of silly effect where a ram is strongest when almost completely sleeved by other modules. I suggest making rams exempt from the usual structural bonuses effects. In other words, make it so that unique amongst modules, ram module hit points remain constant regardless of adjacency (and probably boost them a bit too while you are about it :-).
5) Regarding your "big ships have weaker hulls after some threshold tonnage" idea, I suggest the initial threshold should be 7,000 tons. The reason I say this is that I think the most disadvantaged cost range is about $4000-6000. Smaller ships work well in swarms and larger ships achieve economies of scale. I calculated the average weight of five quite different $5000 designs and came up with an average of about 7,000 tons.
and moving to the edge of trivia....
6) Provide for an optional motto underneath the coat of arms. This motto could be tie in as the (previously suggested) customised exclamation that crew members make when they win a victory.
7) Some thoughts for alternative battle GUI ship fuel, ammo, water, etc displays:
8) Arachnids is a bad name for infantry, given you already have Spiders.
9) How about changing the broadside achievement to firing 5 heavy cannons at once. Having 10 gives the wrong impression that the game is about fielding supergiant ships. As a corollary, maybe add an achievement for winning a battle for each of the first six cost levels (200, 500, 1000, 2000, 5000, 10000).
10) I think it would be nice to allow multiple crows nests if they are at the exact same level. Because it would a) look nice in certain situations and b) give an option to pay for redundancy. Possibly you could also allow multiple dorsal/ventral turrets as well. (The idea being that you could have 2 ventral at the same level, but not a dorsal turrent and a crows nest).
11) Make sure you include the ability to disable the portraits popping up with messages - they seem like a net negative to me (!). Well, I guess they are probably a necessity for developing adventure/campaign style stuff..