I like this sub a lot, and I took some notes for things I would personally change (things I actually did tweak in the editor for my own tastes). Some of these things relate to a general polish or QoL, and some of the changes might stray from your vision and affect the intended balance of the sub, so take what you like and leave what you don't. This could get to be a lot, but I want to be clear.

First, on the latest version I noticed a PUCS and a Backpack (from Backpacks mod) spawn near the captain. Is this intentional? I happen to have backpacks installed and active as well but not sure if this is intentional.

Sprite Depth:
-The background in the top airlock might have incorrect sprite depth unless it's how you intended. That background appears in front of the button on the inside, so while the button is usable it is invisible, and when the door is open, the background appears over the door "frame" or track/rails it's supposed to slide on.
-This may be a design choice, in the Gunnery/Magazine, the stairs are probably supposed to appear as background. When you walk up/down them, your character appears in front of them as if floating above the stairs. If it's intentional, it's a trade-off I guess. Seems like something the developers may want to fix, make stairs always appear above any character that is walking on them.

-The small lights that show the states of switches and things like that (e.g. ballast drain switch, periscope toggle): They are interactable and sometimes when trying to flip those switches, I have accidentally clicked the light and opened the color changer interface. This may get in the way and become an annoyance. Maybe make those lights non-interactive.
-Along those lines, most of the switches and buttons are able to be removed (holdable: can be picked is on), not sure if that's intentional. Not a big deal as it doesn't get in the way of anything and maybe you leave them like that for more options for players.
-Just my tastes, maybe, but the periscope toggle lights feel like it would be nice if they gave off a small amount of light and had the glow effect, instead of "draw behind sub" or whatever it is. When the lights are off, it just adds a little immersion. But maybe it's a design choice, for more performance.

-The bottom Aux. Airlock, those two emergency lights are white and for consistency it feels like they should be red to match the top airlock. When playing with line of sight on, it is just a further warning to players that outside that hatch is the open waters.

-Maybe another design choice but I feel like the two "central access shaft" hulls should have the "Avoid Staying" tag, as it just feels weird seeing AI stand there in next to the ladder.

Supercapacitors:
-Unlike the batteries, the supercapacitors are not linked together; they don't change their recharge rates together like the batteries do. Not sure if this is intentional, to let players maybe boost the railgun power and leave the rest normal.
-A recent update changed the power draw of supercapacitors and while they start fully charged, maybe have their starting charge rates at 50% instead of the full 100%.
-A suggestion for each supercapacitor: the "Msg" interaction message, I would put text telling which turret or discharge coil they are attached to, so at a glance people know what's hooked up to what, like "Bottom RearTurret, Top Rear Turret, etc". Hopefully that makes sense.

-The Aux Sonar Monitor, perhaps labeling it as a mineral scanner in the same way (interaction message) would be a nice small QoL feature, especially if people are joining in MP who haven't read about the sub here on the workshop.
-On sonar monitors, I don't really know how much of a difference it makes in most games but they aren't set to actually use the transducer. Not sure if they should be, or if doing so will give players (traitors?) more options.

-Perhaps on the Aux status monitor, give it the ability to read oxygen levels but leave the main/Captain's one as it is. Gives engineering crew more information to monitor for repairs

-The switch to toggle fabrication: it says "Power Draw 1500 kW", which would be 500kW per machine? But the medfab apparently only uses 100kW, while the deconstructor and fabricator both use 500 each. On the number readouts, it sure enough looks like 1100kW when using all 3 at once. Went from ~1700kW load before to ~2800kW after if I'm remembering right. Maybe intentional, you have that as a safe overestimation?

-This would be more like an upgrade, but like I noticed the PUCS suit now in the command room, I was thinking as perhaps an upgraded version or a "deep diver" version, an extra suit locker + O2 thing on the floor, horizontal, right where the PUCS + backpack are. It seems there is one relay component near the O2 machine that has 2 more wire slots for power, that could go to the locker and O2 container if you were to add this.

Balance:
-With all the nuclear safety features (auto controller, SCRAM, blast door lockdown and water pump for fire), it seems like a reactor going critical and a meltdown is a near impossibility. The reactor might be a little OP. I was thinking of making the fire and meltdown timers a lot shorter, maybe like 15 sec Fire and 45-60 sec Meltdown, to add a little danger if that ever were to happen; and perhaps make it take a little longer for repairs (a few extra seconds maybe). And with all the extra fuel rods to start, it could maybe stand to be a little less efficient than the standard 0.200 efficiency. It could stand to eat through the fuel a little more since you can just throw up to 4 rods at once and let the auto controller do the work.

Small polish?: Terminals for charge rate would look cool with a welcome message, like "Set Charge Rate (use multiple of 10)" or something.

Finally something I have yet to fully understand but apparently the AI can be improved with regards to inventory management and clean up if tags are fully utilized. I know you can set the container tags and have auto-fill randomly place items from a list, not sure if that's related to the way AI detects items and proper places for them. A lot of people don't fully understand the system, myself included, so custom subs have AI that don't do clean up like some of the dev-made subs.

Again, great work and I just want to see it get better! I would be interested in helping playtest the sub if you could use the help. Thanks for making it in the first place!