I wasn't going to comment, but I wanted to respond to the first point specifically, and then I got carried away.

even though fighter factories work just fine in building armored vessels (but can't build unarmored vessels).
(snip)
but god forbid I want to launch a 10ish-ton active sensor into orbit like we currently do for modern day satellites
This is not correct. The design below is essentially a sensor that sits in orbit and can be built in 3 different ways.
1) With fighter factories
2) With construction factories (and a spaceport)
3) With a shipyard
Sentry R1 class Sensor Outpost 229 tons 11 Crew 34.2 BP TCS 5 TH 0 EM 0
1 km/s No Armour Shields 0-0 HTK 4 Sensors 5/5/0/0 DCR 1 PPV 0
MSP 93 Max Repair 10 MSP
Drengr Control Rating 1
Intended Deployment Time: 3 months
Active Search Sensor Std Rng 08.6 Res 10 (1) GPS 100 Range 8.6m km Resolution 10
EM Sensor Standard 05 (1) Sensitivity 5 Detect Sig Strength 1000: 17.7m km
Thermal Sensor Standard 05.0 (1) Sensitivity 5 Detect Sig Strength 1000: 17.7m km
This design is classed as a Commercial Vessel for maintenance purposes
This design is classed as a Space Station for construction purposes
This design is classed as a Space Station for auto-assignment purposes
On other topics
(generally money)
I don't understand how people deal with money, I alternate between having too much and CMCs pop up everywhere, then the bottom falls out of my economy and I now have 40% of my construction building 150 finance centres and hope I don't go bankrupt while they get built over ~3 years.
(generally) Renaming FACs and Fighters
Renaming FACs and Fighters to 'Boats' makes a certain amount of sense (and sets expectations which is important) but I object because 'Boats' sounds worse. 'Small Craft' is a bit too unwieldy. 'Sloop' or 'Brig' might work, less likely 'Yacht' or 'Dingy'. But sailing ship types might not set expectations correctly. Maybe 'Planes' would work? Maybe not.
Anyway if we're going to rename anything it had better be swapping Commercial and Civilian so that all of that finally makes sense.
(generally) Adding maintenance for Commercial ships
For initial balancing my suggestion is that you only count 10% of the mass of commercial ships, and/or have commercial ships use MSP at 10% of the normal rate during upkeep.
But please don't do it, I have enough trouble keeping my military ships in maintenance.
doesn't make sense that commercial ships can not install large sensor arrays of any sort despite modern civilian shipping having radar and sonar almost universally available
I'm not an expert but I am fairly sure that IRL there are huge differences between military and civilian sensors. I have previously wondered if the 50T limit might be too large given the changes to sensor range in C# 1.0.
(generally) Armoured ships should be military
If it was limited to 'ships with armour 2 layers or thicker are classed as military', I don't think this would be completely insane. The biggest problem I see is trying to move 1m tons of ground units to invade someone's homeworld, which I suspect would be practically impossible if the troop transports used maintenance, and unarmoured troop transports are lunch for hidden STOs.
(generally) You can't use components with fighter factories or ground factories
This is for balance even if it makes me sad sometimes.
(generally) Spaceports build all ships
This basically makes spaceports replace shipyards, shipbuilding is currently strictly limited by shipyard type and slipways and tooling. This is a core gameplay feature so you'd need to replicate it somehow.
Everyone seemed focused on a purely offensive comparison between beam and missile fighters. A fast fighter with a high tracking speed and fast-firing guns is ideal for point defence. Missile fighters have no defensive capability.
Missile fighters don't have direct defensive capability, no, but they're frequently used to launch missile strikes from outside enemy missile range, so indirectly they're often extremely capable anti-missile defense.
To be fair, beam fighters can do that too. It's just if beam fighters are used as long range strike capability they tend to take heavy losses and missile fighters don't. So my gut feeling/limited experience is that beam fighters don't have a strong campaign scale logistics advantage over missile fighters or beam/missile capital ships, but I'm willing to see how it works out in practice.
Basically compare the BSG campaign with the 40k campaign.