Someone showed me this game a few days ago and I've been having a blast with it - FTL was fun enough with just oxygen and power, and now I've got water and pressure and a nuclear reactor to play with.
I think the biggest thing missing right now is challenge - enemies get taken out with a press of the space bar, and even if you let yourself get damaged the sub is almost unsinkable when you're surfaced, or when you're submerged and open all the doors and turn on all the pumps. I'm definitely looking forward to convoys and enemy submarines.
As far as minor issues my biggest complaint is how repair works right now - two separate guys always have to run to every object, one to diagnose it and one to repair it, and often reaching a component is so hazardous you want one man to do both and have to coerce him into it by locking doors.
Here's my latest run, inspired by your comment explaining the reliability system, I set mean time to malfunction at 2 seconds. This gives a few minutes until the reactors explode - they fail too fast to shut them down - and a few minutes more until all the battery power is gone, so you have to abuse fast travel between nearby ports like East and West Germany in order to sink anything. With all vents open, all fire suppression on, and the command center staffed by SCBA men, you can render yourself almost invincible to anything except unlucky nuclear reactor explosions that blast too big of a hole in the wall.
Also, one question: I tried desperately flooding the nuclear reactor with seawater once to cool it down, but it didn't have an effect - is that something that isn't modeled, or would it be ineffective in real life too?