Okey to be truthful i havent read all 98 pages... but i thought id leve a word in now anyway, it might have been said earlyer...
How about Capital Ships?
With a limit of 1 Per race, hand giving it a size double of what your biggest current avalible ship class... say if you can build 500kt Cruisers, you could build 1 1000kt Capital Ship. hence you could have ships that really weighed in in combat!
Offcorce the price for these would be high, probably even more than 2-4 ships of the base class(eg the 500kt cruiser in the example)
Having coustom models for the Capital ships would be nice.
And maby adding some special bonuses to these ships, like better accuracy or somthing(think that the best captain would be on it)
My second idea is just more or less to have the ability to start with no tecnology at all, eg to build a colony ship you would need to research the followig: Dome colony(for apropriate planet type)(and for it should be cheap for your type of planet, but very expensive for others), Engines(basic be that Chemical or Ion), Basic ship components(Brige, Crewqt, Lifesp), Basic Cargo bays(if you want them on your colony ship, i usually do)... and then for fighters and so on we would need weapons and sensors and so on... maby actually make sensors and computer non kt dependant(just influenses the cost)
Maby be able to select diffrent materials to build the ship out of? and have these having different properties.
ex. on a 150kt ship.
Steel: Standard, pruduses a ship at standard cost with 150kt.
Aluminium: Lighter, 160kt, all components have lower damage recistance, Higher cost.
Lead: Heavy, 140kt, all components have higher damage recistance, Higher cost.
And loads of different researchable armour/hull types ofcourse, and the increased/decreased damage resistance is to simulate base armour.
Well thats all for now
hope someone likes somthing of it