On the size Issue:
I would prefer the ships to keep the larger size. A Cobra class destroyer is currently 800m long, if it was 800ft long it would be the same size as the Yamato. I just don't see a ship of that size being big enough. The rear third is engines and thrusters and in the remaining two thirds you have to have missile silos (torpedoes) a weapons battery (imo greater than Yamatos) and enough supplies for many months in space. Already it is quite cramped and to be useful to rogue traders you would need additional space.
Crashed/landed captital ships have become basis of cities they would to be fairly large. How large is your CBD? Compare it to a cruiser about 3km long.
I would also like to keep the fluff consistent between sources. I think the Cobra was 800m and the Lunar 3600m before the Rogue Trader RPG.
On Components:
I too would would like components to be more clearly defined. I would see Barracks being support facilities for a company of troops.
On Crew:
I would like a way to improve crew ratings, even if only on select areas. For example getting a better Navigator or better trained gun crew. Maybe each ship or component should have a minimum crew amount and you can't voluntarily reduce the crew below that. You may have thousands of crew on the ship but most are a little busy keeping the ship running to help out dirtside.