I barely consider Cerberus a galactic army. An army, in the galaxy, okay, but its reach was very limited. It just knew how to attack in very precise and tactical ways. Then, for the most part, leave.
Yes, I'm including Omega here. That place was disorganized as hell and it looked like the only reason why the Council Races didn't destroy it was because there was a value in putting so much of the scum in one place.
The threat of ME3 Cerberus wasn't that they could occupy or destroy major planets (even Benning was more of a Smash and Grab, and Eden Prime lacked defenses), but that they could attack anywhere without warning and kill your leader and their staff, and swipe a datapad with more info to advance their particular plans. No threat of them directly rivaling any major military, even one occupied by Reapers.
It was Bioware's problem that we fought them over 1/2 the game, when it properly should have been 1/4-1/3.
Maybe Bioware should have also made clearer that with the Reaper tech and personal upgrades from that tech, Cerberus was pretty much filled with near supersoldiers. Just near super soldiers that still couldn't stand up against Shepard, his allies in concert with each other, and N7 groups that were fighting for their survival, not just because a voice in their head told them to.
EDIT: Oh and I found it weird how little 'indoctrinated agents' mattered in ME3. We have lots of implications of things (like refugees being part of the Reaper takeover of the Citadel at the end?), but few clear examples outside of Cerberus and that one Asari. Hmm. :S