I wasn't thinking about weapons like bazookas or mini-guns, but more along the lines of laser-weapons, knives and such. How else are we supposed to deal with the occasional alien threat?
So here are some additional things I thought of. The low level starting character only has very basic equipment; no weapons, a basic tool-set (think of your standard Swiss Army Knife or Multi-Tool), and small ship with very limited storage space. At lower levels, he gets sent to find lost shuttles (in which case you actually fly your ship around a nebula or something), repair small damaged ships, etc. These typically have one problem, and the chance of alien encounters is low. At higher levels, he gets assigned a bigger ship with more storage, and gets sent to deal with bigger problems, like empty (huge) space stations, deserted moon bases (Original Doom references here please), and similar tasks. There should be multiple problems/mysteries to solve, and alien encounters more common.
As for the Aliens, there should be a large range of alien types. I'd love to see everything from the aforementioned sentient gas to Predator type run-and-guns to that Alien from the Aliens movie that moves around in the airshafts, occassionally dropping down and surprise-sexing you. Facehuggers would be fun. The little bastard latches itself onto you and the screen goes blank. When it clears, you are somewhere else on the ship. You have a limited amount of time to use a medical device in the med-bay to kill the chestburster before you die.
I do like the idea of customizing your own ship, and space-walking excursions are a must. How else am I supposed to repair the coms-antennae?
Another idea: Special, non random levels, drawn from other games/books/TV shows. I think it would be highly entertaining if our little space-buddy stumbled across, say, the space ship from the second Trilby game- complete with Jon Defoe chasing you around.
*Edited 'cause I can't type for shit.