
First off, why are the aliens invading/attacking? The reason may define their weaponry very well. Also, can you explain the alien's attitude towards battle in general?
For example, in the case of a research, aliens may be equipped with what I would call "glue-hose". Essentially, a hose that spray very quickly drying, cement-like material that may stop any potentially interesting specimen with minimal harm. A lethal backup weapon may also be useful if the thing fails.
Alternatively, if the aliens want to eliminate a city without regard of damage, they would just throw some rocks from space, ie, orbital bombardment. Very effective and devastating, and surprisingly easy once you are in outer space. In case of your typical magically-propelled UFO, its easy. Intercepting such targets may be a plot-point in the game, although, for smacking incoming asteroids I think an ICBM may do the trick. Or not?
Also, robots can be great shock-troops. No sense in wasting powerfully augmented warriors to battle enemies, when a hoard of mass-produced automatons can weaken potential enemies.
To run it down, sending in warriors on foot, like in X-com, is only worthwhile if you want something from an area. In the case of a city, possible persons like important people or intellectuals, or materials and resources like fuels from an atomic plant. To cause damage in general, is not worth it.
An attitude that you should keep in mind, is that any soldier or experienced warrior would rather choose simple and reliable weapons over complicated ones. That's why plasma weapons are worthless: they are overly complicated thus unreliable, ineffective compared to weapons like lasers or conventional firearms and just plain pointless. Beyond that, the more fire-power one has, the better.
I also recall from a sci-fi book, that if you spray concentrated oxygen towards an oxygen-breather's nose, it will make them sleepy. Or was that carbon-dioxide?
For more hints, I recommend to study this site: http://www.projectrho.com/rocket/index.html
It's mainly focused on futuristic rockets, but stuff like aliens and side-arms.