I'm not sure what you mean by "rogue factions" of Cerberus.
In ME1 Cerberus popped up everywhere as an organisation of essentially pro-human extremists, responsible for torture, human and humanoid-alien experimentation, wiping out entire colonies...
In ME2 suddenly they were ok to work with, because the Cerberus guys that were deplorable maniacs in the first game are explained away as "rogue cells", or excused because they didnt know the Rachni they were experimenting on were sentient, or all sorts of excuses.
The most agregious problem is the Sole Survivor background you can pick for Shepard. You can find out in ME1 that this was another Cerberus plan, where they deliberately fed the patrol to the Thresher Maws and wiped out every last one of Shep's squad mates. As far as Im aware in ME2 you cant even mention this.
The good Geth thing was.. meh.. but I think it added a lot of depth to the world of the game, I'd rather there be "good" Geth and "bad" Geth than just uniformly "bad" Geth. That's too one-dimensional to me.
I can see how it could provide depth, I just really disliked the retconn. The Geth in ME1 were presented as a hivemind AI that was dangerous and attacking the Citadel races. They had a good backstory about how the Quarians had grown fearful of them and forced them out, making them hateful. They had a monolithic mind, but were a sympathetic villian.
Suddenly in ME2, just as with Cerberus, you find out that the Geth youve been fighting arent the real
Geth, the real Geth are actually not bad guys and the ones you have been fighting are just a rogue faction.
If they had had those things in the story from the beginning it would have most likely been fine but the sudden changes with no foreshadowing, in quite similar ways for both Cerberus and the Geth, felt lazy to me and also undervalued the ME1 story. Cerberus, the Geth, and the Husks created by the Geth make up the vast majority of the enemies in ME1 and suddenly they are just rogue factions and misunderstandings and Shepard is just an ignorant grunt who had no idea what was going on.