Well I went back to the planning board and figured that I just have to set some house rules regarding hull points usage if I wanted to make some sense of the ship roles and fit the largest vessel types into my fleets.

So basically tiny ships stay as fast attack & patrol craft and small hulls stay as corvettes or escort craft. But on medium I figured I could restrict the frigate types to use only 75% of the available hull points. That way they stay slightly above small hulls and benefit from the HP pool of the medium hull. Then the destroyers use all the points afforded by the medium hulls. This way I can either make both equally sturdy/brittle but up the firepower of the destroyers or give both the same firepower but make the destroyers slightly sturdier.

The large hulls are also split in two with the light cruisers again using around 75% of available hull points. Like with the corvettes and frigates, this makes the light cruisers only a bit larger than the destroyers but gives them the benefit of larger HP pool, making them more suited to solo operations when the frigates and destroyers are definately dependant on staying in squadrons. After light cruisers there are naturally the heavy cruisers and the light carriers, both using all the available points. 

A similar duality exist in the huge hulls. Again battlecruisers use about 75% of the capacity while carriers and battleships use it all. That difference of 25% works damn well with the huge hulls, usually making the battlecruisers as formidably armed as the battleships but with weaker armour. 

Of course this still doesnt completely make sense of the AI ship classes encountered, but the contrast isnt as great as it was before. Now the explanation that the vessel types are classed after the purpose of their mission instead of their size makes more sense. 

All in all this means that my shipyards have even more variety and ships to choose from.

I did at first, but it didnt really work out and create enough of a clear cut difference between the different types in comparison with the large hulls. Battlecruisers became just heavy cruisers with more HP, not distinctive enough.

Honestly I've had the same gripe with vanilla GalCiv2 and 3 since I got GalCiv2 back in the day. For example on large hulls you got destroyers, cruisers and battleships all in the same. What this game needs is a sort of deeper role selection for the ships, so that you could specialise them. I know I know, you can already plan them the way you want but that's just it. Right now we have no fleet formations or higher fleet management. There's no real incencitive outside roleplaying or flavour to design things other than the biggest or most easily mass produced and hardest hitting vessel. I've thought more than once that this game should borrow a page from the book of "Sword of the Stars". The first one, naturally. That game got fleet management and ship roles inside the fleet pretty spot on. What we now have is like grabbing a fistfull of random stuff and throwing it at the enemy. I'm not saying that we should be able to micro battles. Instead we should have more control over the fleet BEFORE the battles with fleet formations and ships with set roles that assist the fleet when they are in their spot in the formation.

Oh yes, targeting/protection roles. But I mean turning them into something more concrete. Now you can have a fleet full of escorts and in the end nothing really changes. I'm talking about defining formations for your fleets, either custom for every fleet if you want to or setting up some general quidelines for them all. Then the ships fulfilling their roles in the fleet organisation/formation would possibly give bonuses for the whole. Got frigates, destroyers and light cruisers in a picket line? Slightly more sensor range. Destroyers on capital ship formation flanks? Tiny bit more... something (defence? accuracy? jamming?) for the capital ships. Got a solid wall of capital ships? More attack or staying power as long as the formation holds. Stuff like that. 

This is not something that I care about. Names like, "Frigates," "Cruisers," and "Destroyers" are arbitrary and useless to me. The only thing that I see are capacity points (and aesthetics) and plan and build accordingly. I do not care about the other nonsense because this game is FAR from needing that kind of effort in its ship formations. Only assigned ship roles and weapon/defense specializations matter.