[Darkwind]

I think the solution to the ship problem is to make spaceships cost a lot more. Maybe 15 upkeep for a basic, recruitable ship, with a capital ship armed to the teeth costing as much as 100 gold per turn, as well as quite a few gems. Troops would likely be slower in space and less accurate, so there's an idea for you. Also, militia are essentially raw recruits from the general populace who likely don't even know how to handle a gun or have any useful weapons, useful only because they're easy to produce. Militia in space would likely have practically no mobility, very little precision, and low health (due to the harsh conditions of space and their inadequate armor). At least that's the way I see it.

Finally, Neoclidia and HB's Aboleths are fairly different, though both borrow somewhat from the same source material. Neoclidia is centered around the idea of the Great Old Ones and their awakening while the Aboleths are, well, undead fish-things spewed from a black hole who create pylons which use said magical hole's energy to summon various undead critters from worlds sucked into the hole, among other things. Two completely different ideas.