The number of grunt soldiers makes some sense, though I still question it because of the issue of time. It's only been a few months since ME2 and nobody needed Sanctuary until the Reapers arrived. The bigger issues are manufacturing and logistics. How did they get all their ships, weapons, armor, gear, and mechs made so quickly? How did they get enough people in position to take over the Citadel like that? I suppose Udina can use his position to get some of that done but it's still a stretch for me.
I see where you're coming from as far as gameplay if you like fighting Cerberus better. I do too since their troops have a bit more tactical variety to them. However, from a story perspective it's wrong. The Reapers should be the primary antagonist. It's not like Dragon Age where the Darkspawn army is way in the south while you deal with Loghain.
Yeah, I remember some threads about this topic, many said it's not believable.
As for how to take over the Citadel. Hm, not sure if it could be argued that since they strike at the heart of C-Sec, they have the upper hand in a surprise attack and have no real trouble fighting the officers. The people on the Citadel were portrayed as too relaxed the whole time (James and Joker mention it and generally you have the impression people live in denial bad things can happen on the Citadel), guess that could count for C-Sec as well. Plus Cerberus mooks are heavily armored, while the C-Sec staff isn't. I would think that this has a role to play as well. And I remember a dialogue with I believe it was Thane from ME2 where he says that he sees lots of security holes in C-Sec, seems they are not so well organized as they should be 
Yeah, me too, I love how they can easily flank me if I don't pay enough attention and it keeps the fights really interesting and tactically varied, like you said.
I'm not fully agreeing on it's wrong for the story. On one hand, yes, Reapers should be our primary focus and enemy, but on the other hand, since Cerberus opposes Shepard so hard and tries everything to stop the efforts to unite the galaxy, I'm okay with how it goes. TIM really went to more extremes in this game, and his desire to control rather than destroy shows again and again. That, and that of course he is indoctrinated, likely thinking he is doing all of this for himself when in reality it's probably the Reapers' influence to a certain degree. It's never clearly stated obviously, but using him as a source to oppose Shepard, I can see it.
I've never bought the reasoning that he wanted to get control over the fleet. Udina is an usurper and a criminal. He allowed a terrorist attack on the Citadel and helped perform it. Did he really think the Citadel fleet would just pack their bags and head to Earth to throw themselves at the Reapers just because some criminal scum who violently took control of the Citadel said so? It doesn't help we never get to find out in the game. As far as I know, this info is only in the codex. (Neither the Council, nor Shepard, nor Anderson and Hackett, nor anybody else understands it in the game, but the codex somehow magically has an explanation.)
You get a bit of information on this from Bailey, directly after the coup. Shepard asks if Udina really expected his takeover plan to work and Bailey says it looks like it, and that they sifted through the evidence and that he will send a summary.
As for how Udina thinks he can proceed, I guess we don't know enough about it, but the codex entry suggests it has to do with emergency powers. Not sure what they do, but it seems he thought he could achieve this.
Now, of course it would've been nice to get all this in form of an e-mail and not a codex entry, that would've probably sufficed.
Though I don't sweat it, interpreting the happenings is also a lot of fun 