This is an idea I've had for a long time, but since playing MOO2 recently and remembering just how important it was to my ship design choices, I thought I should post about it before it slipped my mind again.
In my opinion, besides things like special abilities which aren't really *that* important, one important thing MOO2 has over GC2 is the ability to place extra items on a ship beyond what it is normally allowed. You can research miniaturization, but that's about it.
That's one aspect of MOO2 I really liked, that you could spend extra for Battle Pods and increase your available space by 50% while also increasing price significantly, or not use battle pods and get a more budget-oriented sensible ship design.
It gave you the feeling like you have the flexibility to be a "Zerg" design philosophy race, with lots of cheap small ships, or an "Borg" design, with fewer but massively powerful ships.
I think this could be implemented in GC2 by allowing extra items to be added beyond the ship's capacity limit but at an exponential cost increase.
So let's assume you've got a ship with 100 hull capacity, an engine that uses 20 capacity and costs 20 credits, and a weapon that uses 10 capacity and costs 10 credits. If you want to be sensible you could have 2 engines and 6 guns. Or you might want a fast harassment ship, 4 engines and 2 guns. All of these would cost 100 credits to produce. Or maybe just 3 engines and no weapons at all for a cheap disposable scout at only 60 credits.
But on the other side of the spectrum, you could also have a few "Guardian" ships, the flagships of your fleet, which have 3 engines and 14 guns. That's 60 capacity for the engines and 140 for the guns, doubling the ship's stated capacity, but at great cost. For every percent of components placed over the 100 limit, the price of all the components rises by 1%. There would be an absolute limit at some point, maybe double the original capacity. In the case I just presented, the ship would cost 400 credits (60 for the engines, 140 for the guns, multiplied by 2 because you are at 200% capacity.
Balance-wise, if the cost isn't enough (but remember you're taking a ship that requires 15 weeks to build and making it into a ship that requires 60 weeks to build), you could also increas the logistics points a given ship uses based on how much over the capacity limit it is. Maybe have it be something like, "take the percentage over capacity a ship is, divide it by 10, and add that to the logistics. Always round up."
So a ship which costs 5 logistics would cost 15 if you made it into one of these hero units. Maybe you just want a little extra capacity, like 10% more, then it's 6 logistics. This doesn't really seem fair to the smaller ships...
Maybe something more like, this, take an arbitrary number for each hull class and multiply that by [percentage over capacity divided by 10 always rounded up], add this to the unit's original logistics point requirement.
So tiny ships might be 0.25
Small ships 0.5
Medium ships 1
Large ships 1.5
Huge ships 2
Examples: (sorry I forget what the base logistics points are, bear with me, this is only an example)
Tiny fighter armed to the teeth and with fast engines, at 200% capacity.
Formula is 3 + [0.25[100/10]] = 6 (5.5 rounded up)
A small ship at 150% capacity.
Formula is 5 + [0.5[50/10]] = 8 (7.5 rounded up)
A medium ship is at 170% capacity.
Formula is 7 + [1[70/10]] = 14
A large ship that is at 110% capacity.
Formula is 10 + [1.5[10/10]] = 12
A huge ship that is at 200% capacity. Run for your puny lives.
Formula is 15 + [2[100/10]] = 35
These are the best balancing ideas I could come up with as I was writing this post, I'm sure you clever Stardock guys can come up with much better.
This way you could turn your "Terran Flaghip" into a real Flaghip. You would have a lot more flexibility in ship design and wouldn't get stuck needing to research another level of miniaturization because you need just a little more space. You could make real hero units that might survive the entire game, the units you guard your homeworld with. The units that could allow you to actually fight toe to toe with a technologically superior enemy if your strength was primarily economic, etc.