That sounds really cool so far. I would love to make it a sneak-like-game where you have to avoid the enemies because they are so strong (you can fight them, but it's not advised), while also you must solve some puzzles. After some brainstorming i came up with the following ideas:
Sneak-And-Hide:
Like i mentionend before, the enemies are strong and so you have to hide from them and/or trick them to defeat them. They could see you if you stand in the light, or hear you if you are walking on loud floor. Or if you are pointing a flashlight at their face...
Horror-Feeling:
We could make it so that in most areas the levels are dark (not completely dark however, just that you don't see everything always), and you have to use a flashlight to make it brighter. Also, a black far-fog would be nice (so that the player can't see very far until it gets dark.) Imagine pointing a flashlight at some alien and then it discovers you... that would be wicked!
Lights and Sounds:
We could make it so that some machines can be turned on and off, so that they for example make noise or emit light. Which could then benefit you while your hiding from the aliens...
The PDA:
I would love it if the PDA has a central role in the game. It could have the following attributes:
-It is a small light source if it is turned on/used. It's not really much (the flashlight is way better), but it's enough so that others may see you, so you must be careful when you use it!
-It needs energy if you use it.
-You can recharge it's energy at various recharge-stations in the ship
-It holds story informations and story-progress-infos (kinda like a quest-log)
-You can plug it into various Ship-Systems to download information about the ship, the place you are currently at and enemies in the game. Switch this with your idea of the pda hacking into the computer and giving you information throughout the game, and it will be more interesting. We could make the points where you can download the infos hard to get to or hard to find to make them like secret points in the game. (It always encourages me to know that there are secrets to uncover!

). In every level there should be at least one or two of those spots.
-I am not sure about it, but it would certainly be interesting to be able to make some noise with the PDA and use it as a distraction... (but then again this could be just a gimmick)
Portable Life Generator:
Can be filled with the repair-life-form you mentioned and has one use until it has to refilled. It will create a small area where you can regenerate your health... But it makes much noise. You do not have this in the beginning, but can gain it throughout the game.
Please tell me what you think!
Everyone can see the difficult, but only the wise can see the simple.
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