That is, IMO, the silliest argument I've ever seen.
OF course, we are dealing here with the problematics of having a supposed RPG where people are "free" to do what they "choose" and the limitations of a very specific story the producers want to tell. To make possible the arresting of Cerebrus would mean to basically create two completely separate games, and there's no way that would be possible at all.
So the argument falls apart, in the sense that in no way you would get that choice. If you try to play the game as a "free universe" then of course you will be disappointed, since that's in no way ME2. So your argument's best pathway would be to say that since we don't really get to have that decision you speak of, then the whole plot should be scrapped.
Well I disagree. I think that a plot where you continued to be an Alliance commander would be dull. To place the player inside a suspicious organization is clever writing, and the continuous doubts Shepard is forced to encounter (Jack's past / OverLord / ship fight with the quarians in the past / etc ) is cleverly countered with "excuses", but there's just too much out there for it to be coincidental. Shepard knows Cerebrus is bad weed, but at the same time, his only alternative is an Alliance that denies the existence of the reapers themselves.
This is the main driver of Shepard's choice to remain with Cerebrus until the defeat of the collectors. He is given resources, data, intelligence, everything he could ever want to fight against this new threat, something that the Alliance would *never* give him again (since the Geth threat was pretty much solved at this point, and the "reapers claim" was "dismissed"....).
After the job is done he can't care less of Illusive Man's opinion. He's going against the Reapers, with or without him.
I see no plot hole in here, and I never really got that feeling of "HUH WTF Why am I with CEREBRUS??", since that was clearly the superior choice.
The part about the reapers being turned into something laughable has a point. Harbinger simply isn't as charismatic as Sovereign. Sovereign couldn't care less about Shepard, a lesser mind incapable of understanding. Harbinger, however, is simply put obsessed with Shepard. This is, by far, the biggest flaw in ME2, IMO. A god won't be obsessed with a mortal ant. The second biggest flaw is the fact that no one can take the Terminator seriously. I couldn't. The first sketches about this Human Reaper Larvae were much more interesting (and disturbing), but they reminded Half Life too much, and perhaps because of that was scratched. The alternative was worse, though. Apart from these two obvious flaws, I see no others, and these were, in the "overarching plot", details.