Haha, the aliens are something to be feared for me. Even before 1999 UFO Landing missions were a major disaster for my agents because of superior alien weapons and mind control. Cultists can be a real pain too, but at least you have Alloy Vests (and Shields) that will probably protect your agents from gunfire (well, except "holy shit" enemies like Black Lostus Avatar). Aliens are completely different picture - even Alien Alloy armor can't help againt laser or plasma weapons.
Play your strengths, Avoid night missions but prepare for them with flares, flashlights and Incendiary support.
Concealment can save your soldiers, and spotter/sniper combos moving carefully through smoke can prevent landing craft massacre.
The aliens are meh at shooting, but have really high damage weapons, but they have a distinct disadvantage or equalization with humans when engaged at range.
this combined with concealment gives a good chance of not losing tons of dudes to reaction fire and psi.
if you are really want to screw their day up rookies as reaction fire sappers work... in a brutal we gotta win way.
the Avatars panic way too easy. kill their minions and they flip out and run away letting you stun their stupid ass with impunity.
ninjas are stupid and judicious use of fire, explosives, and mines thins their idiotic "I can be dressed in black under full daylight 1 square away being directly observed and be invisible" bullshit.