One thing that's always struck me as weirdly difficult with the spaceship-bridge genre, but wholeheartedly embraced by generic flight-sims, is custom control surfaces! Everyone wants pedals and knobs and sliders and a big red button in the middle of the console. Kerbal players are notorious for hooking up the most bizarre junk they can find as in-game controls, and the game is richer for it. I saw mention of DMX lighting, but nothing about mapping random HID controls...
Another thing we did playing Artemis, was put the "engineering" station in another room, with walkie-talkies so you had to actually "call down to engineering" to ask them to do things. That should be Teamspeak or something now, I suppose, but having the various parts of the ship in physically separate places (perhaps across the internet?) really adds something, IMHO.