Because the world of Mass Effect had to move on without Shepard, it had to go into a new rhythm and force Shepard out of the picture so the Reaper threat can have a justification for being ignored, and bide some time so it looms closer.
And as for Cerberus, it was the only game in town who was working to actually prepare for the Reapers in that regard, so Shepard played the game with them to do what he was doing two years prior.
This is confusing the scenario that was with some sort of inevitability. Cerberus as we knew it in ME2 was invented in ME2- it wasn't even a game in town at the ending of ME1. Anyone else could have been just as (re)invented- such as the Shadow Broker as a patron- or we could have had other reasons than total ignorance for why the Council can't help Shepard.
ME1 had a great big Geth invasion and war with the Alliance. That would be a perfectly acceptable distraction for the Alliance and Council while small and independent colonies go missing.
That detour was necessary, because otherwise 2 would be about a Reaper threat that won't be coming in the game. Shepard would have all the resources needed to stop them right off the bat in 3, or at the very least their subsequent invasion would be hit harder, leaving the galaxy in a more optimistic position instead one that's very apocalyptic.
Since the Reaper's strength is arbitrary, this isn't an actual limitation. The Reaper invasion can be as strong as the writer wants to be no matter how well the galaxy is prepared. Moreover, ME2's endpoint is whatever the writers want... and could be such that the crisis is worse and more dire, rather than less. It could even end with a partial Reaper success, which would be an excellent bridging purpose of a mid-game.
Say the conflict of ME2 is with the war against the Heretic Geth rather than collectors. In the course of the war, the Geth (at the behest of the Reapers) make outreaches with the Terminus and anti-Council groups, risking a Terminus War that would divide the galaxy in time for the Reapers arrival, while building some gambit that could turn the war (say infecting the Dyson Sphere with the heretic virus).
Let the Suicide Mission be about breaching the Rannoch relay- suitably impossible for the setting. Let the character missions be about trying to put out the brush fires that could start the Terminus War. Let the subplots be about things and themes that will actually matter in ME3- of Synthetic-Organic conflicts, or Dark Energy, or whatever.
And then let Shepard return from the Suicide Mission, having saved the galaxy in the short term, to realize the Reapers have lit it aflame elsewhere. That the Batarian Rebellions have started, pitting Humans against Batarians, while a Krogan Civil War threatens to launch a new Krogan Rebellion. Let the Quarians- whether desperate or indoctrinated or both- launch a war against the Geth, regardless of the True Geth of Legion.
Let progress be made, and yet also a galaxy divided, so that Shepard's uniting of the galaxy come ME3 comes in the context of a galaxy that was already preparing for war.
The fact that he didn't, and he had to work from the ground up with a terrorist group, is frankly better from a narrative perspective because it allowed the Reapers time to get there. If we had carte blanche or the story was different, what would Shepard actually fight that would possibly make sense? The collectors as a minion threat functioned well enough, despite being a weak villainous group overall.
The Collectors as a super-advanced minion were pitiful because they opened up multiple logic holes- starting with why they didn't help out Sovereign and Saren's goal in ME1 (where seeker swarm tech would have made capturing the Citadel a cakewalk), and moving on to why they were they acting at all.
There was never any point to the Human Reaper from the Reaper's ambitions- it was never going to be completed without Earth, and Earth was going to be blitzed from the start by the Reapers thus rendering the colonies irrelevant for havesting purposes.
The Collectors were also largely redundant, in that they thematically replicated what the Geth already were in ME1: a secretive, reclusive race behind relays that no one survives going past with extremely advanced technology and unknown intentions. If the Geth had done the harvesting at the Reaper's bidding, it'd make just as much sense.
BioWare's biggest crime is they pulled a fast one and took total control away from the player there for story reasons. But I have a feeling it was also the only way they can actually see the story working from both a game and narrative perspective.
You never had total control, though.