In general, against Exalt, Red Dawn, do missions at night against them. DONT do night missions against Lotus.
Ninjas are hard to spot already, night just adds more insult to the injury.
Scout drones have anti-camo, capable of spotting ninja's better than humans.
I no longer feel much difference to go on missions of factions day or night. I have found enough countermeasures against each type of enemy to fight in both light and dark. And yes, assassins are always equally well disguised and usually I take a rat against Lotus, which is much more effective than a drone, especially at night. Although the drone is also present.
One way to discourage grenade throws is to space out your troops. Have 4-5 titles distance between them and its just better to have one guy hit than two. That helps considerably.
Osprey and Kitsune are neat that you can stand beneath them to cover from grenades.
About the separation of soldiers, I think so it is clear.
And about the shelter under the planes. Several missions were such that the whole crowd stood behind the wheels of my plane for a long time, minimizing the chance of hitting me with conventional weapons and not giving the chance to throw grenades at me, and this is also quite a common thing.
A little out of place in this topic, but I wanted to tell the story of one of the last, interesting long battles.
It was the defense of the mansion against the Exalts. On the mission, I took a drone, a rat, 2 dogs and 4 agents with all stats, except for melee combat, maximally raised (for this stage of the game). Armed at the start all with two-handed electric stunners and 2 with MAC-10, 2 with light cannons (first trial). On the first moves, I stunned as many civilians as possible so that they would not be killed immediately and ruined the house with grenades. At this time, the dogs stood in the courtyard in front of the doors and waited for guests, and the rat simply hid. Then he gradually took all the residents to one of the windowless storage rooms and put the drone inside the room in front of a closed door. When the enemies began to come more actively, I had to move from the courtyard (there is no roof there) into the corridor. But after some time and a dozen or one and a half corpses, the crazy grenadier smashed and burned this room and had to retreat deeper into the building. For a while, it was possible to shoot back, looking through the windows from the room, opposite the front door, but the outer window made me a little nervous, even though the rat with psi-vision illuminated the approaching enemies. Then, with a wrench, i made holes in the walls and placed the dog comfortably so that it would calmly kill everyone who came. On the second floor, there was also a war, and I burned part of the floor myself, and the other part was destroyed by enemies with miniguns. When I had to go to rearm, I put the dog in one secluded place behind a broken wall, in which it is not visible from the street and it easily kills those entering the stairs to the second floor.
When the mass panic had already begun and the enemies stopped coming, i began to inspect the territory from the roof with a rat, broke the wall on the ground floor so that it was convenient to go outside and showered the territory with flyers. Two armed with sniper rifles that ignore 25% of the armor and went to the roof. Then a couple of grenades and 3-4 shots of snipers and the armored car was destroyed. Victory with 2 dead civilians who, after the middle of the battle, simply trampled in a closed room.