1. Buffed security
The ability for security (or all people) to grab a person when non-stunned. Perhaps not being able to drag them but hold in place. Whilst doing so security can frisk the person to show their inventory (like when cuffed), perhaps small items like screwdrivers, detonators and such have a chance not to show up, where multiple frisks would be a safer option, but when you are just examining the crew perhaps it may slip past a guard.
The ability to lock cuffs, as it stands anyone can remove handcuffs at the moment, it leads to many annoying situations where people being cuffed (for a reason or not) cry out for help to fellow crewmembers to uncuff them. This is annoying as absolutely anyone can do so, and take the cuffs for themselves, on most subs there is a small amount of them aboard. With the option to lock cuffs they should be able to be removed without keys somehow, like having someone else use a plasma cutter to tear them off.
Third, a reworked way for the harpoon gun to work, currently as it stands over 50 weapons skills allows you to shoot in a straight line always, its not hard to aim straight and there is 0 reason a spear would shoot out at 30 degrees from the muzzle. The way I think would be nice is firstly the need to add compressed air to the harpoon, either adding to the muzzle velocity or requiring it to work, perhaps harpoon guns should also have a barrel slot on them, weapons skill would automatically place a new harpoon into it, whereas less experienced would have to do it manually, which would take more time to fire a full magazine of spears.
I also thought an idea of being able to "aim" the harpoon gun (with enough weapons skills(?)) would be cool.

2. Knocking out and stunning
Being able to knock people out with blunt weapons (wrench, unpowered baton, perhaps c4 when not lethal) would be pretty cool too, as you get closer to being more knocked out you begin to be dazed, where your screen either blurs or starts to scramble with white noise, making it harder to notice whats going on, I couldn't really make a mock up of this happening as white noise doesn't really affect your ability to know whats going on, and I have no idea if the game engine would support blurring the screen.
I also thought stunning people could be improved a bit too, where when you are stunned you screen whites out, and if you are stunned enough, blacks out as you fall unconscious.

3. Some weapons with already in use items
The spear (handheld) and screwdriver would both be obvious choices here, where spears do more damage and bleed and screwdrivers doing minor, with a chance to bleed.
4. Radio/Local chat
Something I believe would make the multiplayer experience miles better (not saying that I don't like it, I frequently host and not being able to play as I spectate moderate is somewhat annoying, the internet communities fault).
I have no idea on the radius talking should be, but I thought if radio chat gets implemented that it should only be displayed as either; Radio: [chathere] or Radio[Channel]: [chathere], with all chat coming out as a continuous stream, so to effectively make use of it, you would have to first identify yourself, and then make a clear finish. "X here finished repairing breach over Y the front room just flooded over". Where not doing so would end up as "finished repairing the breach the front room flooded". Which could end in disaster as messages get mixed (which of course is fun).
Whatever happens, im loving Barotrauma so far. Keep up the great work Regalis (and that new guy you were talking about)