#1a Rename Fighters as Boats
This point I agree completely.
Aurora really is a narrative building assistant, and so it will be much better if it will not use words, that imply some fixed purpose of small craft you try to build. Especially in early game, those Fighter Factories in some campaigns tend to build anything except fighters.
I'm not a native English speaker, yet it seems that Small Craft and Small Craft Factory are the best words.
The same with missiles. [Guided] Ordnance/Munition Factories and Guided Ordnance/Munition, may be.
Because in early game, where your narrative is forming, those Factories are often build only buoys and probes, not missiles.
#1b Combine FAC's into the Boat category
Not completely agree, yet it's really itching point of strict arbitrary lines, that looks silly -
attention disclaimer! - not because a decision to make this line was ill-conceived, but because of the course of things, because it's really a problem in the nature of game development, and it's hard to break a habit of having such strict arbitrary lines after living with them all your life. Yet modern computers give us a way to avoid this problem!
What I can suggest about small craft definition - is to add for them a mandatory component, something like Landing Gear, which size will grow as k*(craft size)^2 or even k*(craft size)^3, so it will be just inefficient to make large small craft designs.
With such mandatory component it will be no arbitrary line, yet meaningful distinction between small craft and ships will remain.
As for Bridge component - I'll just make it the same as other C&C components: giving bonuses (or bonus multipliers), that are growing with crew size, yet not mandatory above some ship size. Any player will have an option to build large vessels without bridge - they'll just will have poor operation times and/or maint life (yet such a design can be a good choice in some special conditions). Any player will have an option to build small vessels with bridge - they'll just will have poor payload.
#2a Remove the Size Constraint for Commercial Engines
I like a suggestion to give up commercial ships' direct commands. Let AI command them, and if you want to have some ship under your direct command - well, it is then your job to pay attention to it's maint. At least it can be an option at the game level, the same as to switch maint off completely.