Do you not even pay attention to the narrative?
First off, its explained all throughout ME3 how they get their army, through Reaper implants on first volunteers, than abductees and refugees. Thats a major part of the Cerberus arc. Second, they are a force that strikes fast and quickly, but do not have the numbers. In fact, on Eden Prime, two big datapads...
"We've taken more able-bodied men and women from pacified neighborhoods. The colonists generally have accepted the story that they have gone to perform tedious but safe manual labor in a Cerberus research camp on the other side of the planet, and when we increased food rations as "payment for the work", most of the complaints died out.
Maintain the story as long as possible. We don't have the manpower to fight the entire colony, and if these families knew they were never going to see their sons and daughters again, there's no way they'd cooperate. "
and this.....
"Local resistance is heavy in the south and west sections of the colony. We've pulled most of our troops from the north neighborhoods to assist. All remaining troops in the north neighborhood: continue standard patrol activities to maintain the illusion of a large presence in that area. If the locals knew we were understaffed, they could do some serious damage."
So Cerberus does not have as many troops as you think. Why on Omega do they have to use force fields to keep the populace at bay? Also why do Cerberus troops flee when the coup is stopped? Simply put, they don't have the numbers. They have an illusion of a large, powerful presence.
Next, Kai Leng didn't just drop in on Thessia, he was there all along. Pay attention to the narrative.
And finally, Cerberus's increasing numbers ARE justifiable due to the horrors of Sanctuary.
Face it, Cerberus is all about superior intelligence, and light and fast strikes. They do not do so well holding territory or head to head combat against large forces.