Howdy, I've just joined and thought I'd add some ideas:
1. Randomise the layout of the towers. I think this would be fairly easy to implement. Just imagine, with this you could play through a game with a more civilian bent (two civilian towers, some kind of recreation tower), a mining colony (massive central storage tower, mining equipment) or a research station (overall scientific theme).
2. The inclusion of "fresh meat", weak, frankly dim allies which you'd begin the game with; their sole purpose is to get snatched in order to buy you time during the beginning phase.
3. Expanded classes, which aren't designed to be balanced, there would be achievements just for completing the game as each class since each one would be a mode unto itself.
I'm thinking:
Marine
Heavy Weapons Specialist
Scout
Medic
Technician
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Android = A synthetic robot that looks exactly like a human. Since their creation is, I imagine, expensive as Hell, it makes sense they'd be owned by a big corporation, making each one designed for their most obvious use, special operations and recon. They would be much more durable than a human, with a stealthy skill set, but wouldn't be over the top in power.
Worker = An all rounder, begins with some handy tool and decent body armour, all skill costs are average. Since they are native to the tower, they would likely have more fresh meat with them than the other classes, further, they might even be competent to a point.
Prisoner = Begins with very little, but is an uncompromising badass that levels quicker than the other classes. Any fresh meat hanging around the Prisoner would be disloyal, if not outright violent. Choosing this class would obviously generate a prison area of which to escape from.
Scientist = The living opposite of the Worker, they would be able to "research" the aliens in order to better combat them as well as having a "high clearance rating" which allows them to enter sealed areas and get free stuff from wall vendors. They might also be able to convince people to work for them, running on the movie trope that people listen to scientists.
4. Alternate Goals:
1. Kill the Queen.
2. Escape in a ship. Requires others to help man it, a weak victory. May involve a time limit or combat against marines defending it as the place is on lock-down.
3. Rig up a communications station and contact some government body that will send marines to save you...or nuke you from orbit. Bad ending.
4. Escape the towers. Travel beyond the tower in an astronaut suit in a buggy. A fade to black style ending, alluding that this is just a prolonged suicide. Plus it might mean you've let the aliens out into the wilder reaches of the planet.
5. Destroy whatever makes the oxygen (and possibly gravity?) of the towers, killing everything. Another bad ending.
I think, while not exactly missions, would add a lot to the game.
Thats my lot for now, cheers!