Before we talk about how poorly the Cerberus military/Husk armada is I want to talk about how stupid TIM is. His whole plan in ME3 is so stupid.
I don't know how many people we use to build the Crucible but seriously, what did he hope to gain from stealing the data for the Crucible? That he could build it with his huskified slaves? The big problem with Cerberus in ME3 is the logistics of their operations. In ME2 you ask EDI how many there are in Cerberus and she says there's no more than over 150 people in total or so. 6 months later they are in every corner of the galaxy and they send out probably millions of troops in total. I guess it could be justified by saying Sanctuary had been going on longer than we knew or something, but it's just a huge asspull either way.
I was never expecting Cerberus to turn on you as in them becoming a direct opposing force you have to fight. I just thought we would be betrayed in a diplomatic sense and TIM would use his special brand of cunning and inside-sources to get his way. Hell, I expected him to snake his way to power or control or whatever he might've wanted in ME3 by bargaining or something. You find a way to defeat the Reapers and he proposes, dunno, perhaps offering you experiments he made that can give you an edge against the Reapers but then in secret it would be something to advance humanity via Reaper tech, secret Alliance resources or simply the Crucible. The main point is just that Cerberus shouldn't have been a military opposition in the game, but a diplomatic one.