add % to alien stats. if you have hard, normal and easy, then easy would be -10% to stats, normal would be normal while hard would add 30%. You get the idea.
make maps larger as difficulty progresses. maybe double maps. they are pain in the donkey
Introduce alien autoguards (bots?) on harder difficulty levels. To make them simple, cannot stun them, they blow up big upon death (only if no aliens near, otherwise just disintegrate). Maybe some bots mine land and air (invisimines?)
Inabilty to research alien technology until..... this way at advanced levels you dont get to research the best weapon after the first mission.
at high difficulty, aliens can resurrect after certain time.
Random events, maintenance problems, weather anomalies, aliens breaking out of the containment, money loss/grants, these things should come with antiloader protection though.
Antiloader protection, so people dont play by reloading. basically game calculates certain events (random events? some aspects of battle?) a few turns/minutes ahead. So when you save, you save with those strategic calculations
some graphics, texts saved in easily editable files.

Product placement. get sponsors, or if you desire to promote your own companies place names on battlescenes. Just dont overdo it.
Aliens, technology, ray guns and space ships are important. But so is sex. maybe add something of that sort to the game