just a quick couple of points... maybe good maybe bad...
scale :
-frigates - fighters
-destroyers - corvettes
-cruisers / battlecruiser - frigates / VERY HEAVY frigate (battlecruisers could be implemented as being a cruiser with a signifigantly longer build time and resource cost to the cruiser but better over all, so like 3x the build time, 3x the cost, and 2x the firepower/armor.)
-battleships - destroyers
(not sure if it is possible, but if you CAN make destroyers dock (i know in normal HW2 they cant dock) that would be a thing for the mothership - being able to dock battleships. the carrier - which hopefully could be made to dock frigate scale ships (which i realize in HW2 those could not be docked either) would be able to take frigates, destroyers, cruisers/battlecruisers.)
-dreads, carriers, motherships - capital (only ships with jump drives)
dread = only has capital class weapons, and is the only ship that can carry them.
carriers and motherships, the fastest way to move your fleet (jump drives) also capible of docking miners and unloading ore as cash)
carriers and motherships would be the most tank ships in the game.
pos = shipyard class, but immoble. it is the only thing that can build anything bigger than a frigate (could start with a carrier and some frigates?), the pos is also the only thing capible of building turrets/probes.
station arrays = turrets and probes - these will probably be the hardest to get to work right. you will want to make taking out the pos the only way to deal with the turrets. if possible, make an effect that radiated from the pos to all friendly ships and structures and ships healing them fast, but make it very short ranged - it would also have to disable them from shooting while inside the field (maybe something you have to manually activate that costs $$ every second its active)
-essentually i think the pos should be the major 'hub' of the player's operations. it will take a little time to get the resources to build it - until which point the players will really only be able to do skimishes with each other, and ideally the carrier providing ranged repair support (healing 'guns' i assume would be the easyest way of doing remote repair) and command links (HW2 Fire Control Towers - built on to the carrier)
anyways, when a player does get enough material together they can build a pos (maybe some research is required to? not sure what role research is going to play in this) with the pos up, maybe you can build a platfrom that mines things that normal miners cant (moon mining?) as a way of providing steadyer income?
industrial ships would serve as great refining ships.
anyways, with different moduals built on to the pos, you can build cruisers, research battlecruisers, build battleships, and the capital module and then research dreads, carriers, and motherships.
as for capture ships, that might be a neat idea for attacking pos's, but not so much actual ships.
perhapse you might take it to the next level and add outposts as the only conquorable object (needing capture ships) and putting it into multiplayer maps as the only way to build a titan or something.
anyways some ideas, possibly a different perspective.. regardless, i cant wait to try this mod regardless of how it is implemented, get to it!