First I would like to say that the core gameplay feels just right and should not be changed in any major way. It feels oppressive and tense, just like an Alien game should! IMHO it is particularly important that the number of basic actions that the player can perform does not increase too much. You don't want this elegant game to become a mess of unintuitive controls like NetHack is (I don't like NetHack, for that reason and others).
Here are a couple more observations I made about the game:
-It seems that when Elites first start appearing, unless the player has been really lucky and found a pulse rifle early, the only means of defending against them are the Krak grenades... which are also really hard to come by at that stage. I don't think that Elites should be made any weaker, or the pulse rifles come any earlier, but perhaps Krak grenades should spawn much more often on the earliest levels with Elites. I haven't yet tried the Colt against Elites, so maybe that is an option too. Edit: Found out in my last game that the MP5 will kill Elites too, at the cost of much ammo, so it's just the combat shotgun that is useless against them.
-Once the player has a pulse rifle and a heavy weapon, the aliens don't seem to be much of a threat any more. Even the Elites die like flies to the Smartgun, while the pulse rifle takes care of everything else. Even the constant spawning of Hunters all over the place doesn't seem threatening, since there is also a lot of ammo around. I would suggest that at about 100000 turns, Main tower levels 6 and 7 should become far more dangerous (Elites everywhere, hordes of juves in rooms, etc). That should give enough time for the player to get in, kill the queen and out again if they don't waste time hunting for the big guns, but if they do go looking for the big guns then they will need them.
-Health seems to be much less vital than ammo, which doesn't seem right. It's easy to stay at 10 medkits most of the time (except when taking on an Elite without a suitable weapon, in which case it should be "Game over, man" unless you have a krak grenade... instead you are able to burn through 10 medkits to win by attrition, as I did the first time this happened to me). Using medkits during fights is too easy as well. I would suggest reducing the medkit limit to 5, making them take much longer to use (the equivalent of several turns), and making the player unable to use them while being attacked.
-Radiation seems pointless. The health drop is so small that it's barely even noticeable, and there doesn't seem to be any way to defend against it. So I just ended up ignoring it. If you want to give it a little more "bite", you should make the health drain much more rapid, and give the player some way of dealing with it that requires modifying their actions. I've suggested one way to do this on the list below.
New Feature Suggestions
-A save feature! And fix the map generation bug that can put doors too close to the outer walls, please. :-) Also, change the default keybinding for the character screen to 'c', so that pressing Ctrl-C by accident is far less likely.
-It would be really handy to know which regions have been explored. Room or corridor tiles that have been seen could be shown as a dark grey '.'. This way the player would know when they've gone in a circle, or when they've already opened a door and didn't like what they saw on the other side, so shut it again quickly.
-Levels of Fitness skill allowing the player to carry more grenades (1 extra of each type per level of skill).
-Levels of Perception skill allowing the player to see aliens which are 1 or 2 tiles beyond their light radius. For every alien that is in this area, in every turn, there is a chance (5% per level of skill) that the alien will be revealed to the player, without the alien noticing the player.
-Exploding fuel barrels. Does this feature even need an explanation? :) They would go off like grenades when damaged in any way. Found in large numbers in the Engineering and Storage Towers, and often close together so that they can be set off in chain reactions!
-Radiation suits, and accumulating radiation. Change the radiation damage so that it steadily increases the longer that the player remains unprotected on an irradiated level. Also add a new armour type, the radiation suit, which is found commonly on irradiated floors. It offers no protection and cannot equip heavy weapons, but it stops radiation from having an effect on the player while worn.
-Countdown levels. Veterans of the Alien Breed games will know what I mean :) The countdown begins a few turns after entering the floor, with the voice message "Warning. Reactor breach imminent." and from then on all the walls and floor tiles get drawn in red. There should be lots of ammo and grenades lying around on these levels, so that the player can afford to be a bit more reckless with ammo than usual. Once the countdown has started, it doesn't stop even if the player leaves the floor and comes back again. When the countdown finishes, the whole floor becomes saturated with high-intensity radiation that saps the health of the player and all aliens very quickly (at least 10 HP per turn, not affected by armour, although the radiation suit cuts the damage in half). It remains irradiated permanently. The first floor in all towers, and the last floor that connects to another tower, are not allowed to be chosen as countdown levels, but any others are fair game. The 7th floor of the main tower should perhaps always be a countdown level :)
-Armour durability. Each type of armour has a limited number of hits it can take before it is destroyed. This number is higher the rarer the armour type is. For example, the common Flak Jacket can only take 15 hits, while the Power Armour can take 100 or more. Technical skill increases the durability of armour by 25% per level of skill.
-Map terminals. These are randomly placed in rooms. When "activated" like doors, these automatically put the player into an extended version of the "look" mode which allows scrolling the view, so that the player can examine the structure of the map without having to move around. This extended view is only available when the player enters look mode by activating a map terminal.
-Flares. These work exactly like grenades and are effectively a new grenade type. Instead of exploding, of course, they light up an area for an extended period of time (hundreds of turns). Intended for use in the low light levels, where they should also be quite commonly found.
-Flash grenades. These do no damage, but stun any aliens in the blast range for 1-4 turns.
-Grenade belt. When found, it doubles the player's grenade carrying capacity. Maybe this should be an armour type, so that there is a cost associated with it as well.
-Shipping Crates. These are passable, line-of-sight blocking tiles that occur inside large rooms, mostly in the Storage Tower. The player can climb over crates at 10% of their normal movement speed (plus another 10% per level of Fitness skill). Aliens can climb over crates at 75% of their normal movement speed. Crates do not block the sight of aliens. A single crate is placed next to the player at the start of the game, to give the game a "Start to Crate" time of zero (this is a gaming in-joke, if you don't get what I'm talking about :)).
-Rubble and barricades. These are new tile types that work exactly like the shipping crates mentioned above. However they are found in all towers, they are placed in a different way, and they are not found in such large numbers.
-New Alien types. These would only appear well into the game, and some of them not until very near the end.
-"Runner". These are similar to juveniles but have greatly increased speed, so that they are even faster than Hunters.
-"Shadow". These are similar to Warriors, except that they are slower, and invisible until they attack.
-"Leaper". These are exactly like Hunters under normal circumstances. However, if they are within 6 tiles of the player and have a direct line of sight to the player, then they can jump across 5 tiles to land right next to the player. They can only do this if they moved towards the player in the last turn and have not been shot since then, so the player can keep Leapers at bay by shooting them before they can jump.
-"Elite Leaper". Leapers that are as tough as Elites.
-"Tank". These are so heavily armoured that they can only be hurt by explosives, or high-accuracy weapons such as pistols (they have "weak spots" that can be hit for "massive damage", you see, but only if shot at with sufficient accuracy ;)). Tanks are very slow, but they hit hard. They can also break down doors. They don't just open the door like Elites do, they actually convert it into a corridor or rubble tile.
-"Hydralisk". An Easter Egg enemy that only occurs in one place in the game, although I have no idea where that should be. The Hydralisk will keep its distance and shoot at the player, with attacks that are similar to the Colt attack. It is otherwise similar to a Warrior.
-A motion tracker. Once the player has it, the motion tracker "pings" unseen aliens (or any other moving object) near to the player when they move. Line of sight is not required. A "pinged" alien is shown as a green '?'. Aliens that are not moving will also occasionally be pinged (10% chance per turn).
-Automated Defense Turrets. These are randomly placed in rooms in the main, security and military towers, and aliens do not spawn around them (unless they are inactive - see below). They are hard to kill except by explosives, and have a limited ammunition count. Some of these are "safe" and will shoot at the aliens, but not the player. Others are "rogue" and will shoot at anything that moves, but the player can avoid being targeted by standing still. Some turrets are inactive when first found, and need to be activated in the same fashion as doors before they will do anything; it's up to the player whether they want to risk activating a rogue turret! Any inactive turret has a chance of being made "safe" when the player activates it, if it wasn't "safe" already, and the chance goes up with each level technical skill. At the highest level of technical skill, even rogue turrets will not shoot at the player.
-Tazer and Modified Tazer. These are found in Civilian, Security and Engineering. The Tazer is completely useless, and can't be picked up unless the player has at least one level of Technical skill. The Modified Tazer is a short range sidearm that doesn't do any damage, but will stun an alien for 1-4 turns. If the player has the required skill, then when trying to pick up a normal Tazer they will automatically try and convert it into a Modifed Tazer (with a 40% chance of failing, minus 10% per level of Technical skill). Rarely, Modified Tazers will also spawn.
-EMP grenades. These won't be much use unless "robotic" enemies make it into the game (such as the rogue defense bots that Kornel already planned, or the Turrets that I propose above). EMP grenades would disable robotic enemies in their blast radius for 50 turns, without actually destroying them. Their blast radius is big enough to cover most of a medium sized room, so it's hard to miss with them.
Some Tentative Suggestions
These ones I'm not so sure of, because they involve complicating the core game mechanics in some way, particularly by adding new controls or resource types which aren't natural extensions of the ones already there (unlike flares). I mention them only in case they might inspire Kornel or others with new ideas.
-Security cameras, and terminals that the player can use to access them. The cameras would be randomly placed alongside the walls of rooms, and are non-obstructing (like corpses). The player can activate a camera terminal using the space control, like doors. They then enter the camera viewing mode, where they are shown the view from one of the cameras instead of their own current view. In this mode they can cycle through all the cameras on the current floor by using '<' and '>', or leave viewing mode by pressing escape. These controls are explained by a command line message when they enter the camera mode.
-Run mode. This is a movement mode that can be toggled on and off by the player (maybe by "S" for sprint). While in run mode, the cost of movement is halved, but reloading is impossible, and accuracy of firing and grenade throwing decreases. Aliens can also use "run" mode; any alien that sees the player begin running will begin running itself 4 turns later, and will not stop running until it is dead or loses sight of the player. If the player is already running when first seen by an alien, then the alien will begin running immediately. Aliens will not run unless the player does, but will advance slowly as they usually do. The amount of time that the player may spend running should be limited by a "stamina" meter which depletes quickly while running and refills slowly while not running, and is affected by the player's Fitness skill. Aliens do not have this limit, and can run forever.