Let's see, if I were going for design themes, based on your descriptions, I'd go with things like this:
Humans: Bright colored ships (meaning you see lots of chrome and bronze and polished surfaces), sleeker designs, multiple modes of propulsion across the fleet (fans on some, flapping wings on others), if particles aren't a concern, lots of moving parts and ostentatious, superfluous piping and design. Real clean and fast, fresh out of the car wash and flying down the highway. Weapons don't pack a punch, they can't take as many hits (weak hulls), but their little devices (abilities) as you put it, can be used to exploit the others weaknesses to give them the edge they need to win. Maybe have them use magnetic field generators to shield them from enemy fire. (Lots of shielding.)
SubHumans: Design could be similar to human, however with less flair, so to speak, since they probably built and tested the prototypes for the humans just in case the design was bad, no humans would have been killed in any accidents. They would naturally have less to work with and would go with function over form. As their sight is different and they're workers at the core of their being, color is less important to them. Their ships could have a darker, dirtier look to them like they were built in coal mines. More mechanical than lighter then air, and thus able to take quite a few more hits. (Probably also due to the fact they built up safety systems over the years to protect themselves from all of the 'testing accidents'.) More dependent on stronger hulls then shielding if any shielding at all. Maybe make a ship whose ability is to provide shields, or a planet defense structure that grants shielding to ships so those playing defense get it, but those on the attack in enemy territory don't.
MadTechnoBots: Another function over form style, however with the Texan bigger is better mentality. (Besides, it would have to be to house all of them large batteries for their propulsion systems and special abilities.) A lot more weapon points, more powerful weapons, slower movement because of the bulkier designs. The most mechanical looking of the bunch for the obvious reasons. Middle of the road hull and shields. They can often times be outrun, however if they catch you, they'll punish you in several painful ways. If you let them build their fleet up, then you deserve the ass kicking coming your way. Their drawback is that they have few special abilities, and since they are robots after all, personal safety isn't any concern, so ship repairs on the fly aren't available. (No hull regeneration. Repairs can be made with a repair ship that has no offensive capability, or by island side repair stations.)
Pirates: Mix of designs, dirty with piping, spinning gears and steam jets spewing out all over the place due to poor construction and maintenance practices, but also loaded with weapons from all three other factions. "A gun for every situation." style. Smoky exhaust trails, and prone to breakdowns (via auto-used abilities) which can be lessened via research. (Basically, a self affecting ability that shuts down weapons and engines, shields and regeneration if any, all at once, or individually with their own timed abilities, and research would increase the cooldown times of the abilities and lessen the duration giving off the appearance that they're getting their collective $#!t together as the game progresses. This is of course, is only doable if they are non playable as a player could just turn the ability off.)
Militia: Depending on their need, you could probably get away with just reusing the pirate ships since independent colonies wouldn't have the resources of an ever expanding empire, thus they'd be forced to scavenge or buy from the black market. Could also borrow one or two designs from the others as well just for variation.