Set up a somewhat epic late game setup, and have a few suggestions:
Add Gunboats to the fighter Squadrons Window, so squadrons of gunboats can be made too.
Also, an ability/button to print out a fully extended OOB from the Naval Organisation tab in the Task Groups/Naval Organisation tab.
On the Fighter Squadrons Window, can you change the mothership dropdown box to add the class designation of each listed possible mothership, and/or list them alphabetically instead of order created. Another thing which would be cool here is the ability to add each squadron to the Naval Organisation Tab, to the task group containing the mothership they land on. At the moment I create a squadron, designate its mothership, land the squadron then launch it again so I can add it manually (Add TG) to the relevant manually created squadron branch, before recovering them again.
Seconding the Increasing efficiency of engineering spaces:
Larger Cargo Containers, Fuel Storage and Crew Quarters, especially as later in the game the ships get bigger, fuel transports gets especially ridiculous.
Bigger fuel Containers - the numbers of crew required on the larger FTs gets enormous. What would be ideal is the ability to make Fuel Containers in the same way Magazines are made, using Armour, HTK and Size as the variables, anything above 1 HTK classed as military and only available once the relevant level of Armoured Fuel Bunker is researched (I never bother with that as it is as ships generally require a lot of fuel storage and I think (not entirely sure) that it holds a smaller amount than the normal fuel containers).