What’s disappointing about ME2 is just how much it suffers from bridge syndrome - the plot from the first game gets put on hold in order to allow it to pay off in 3, which means that 2 is about spinning its wheels in preparation for that pay off. The third game feels more like a sequel to the first. And a lot of the problems stem out of the fact that ME2’s plot is all about the squadmates, and Cerberus is involved for reasons that really don’t require them.
I mean that last bit. Cerberus was a rogue Alliance black ops group in ME1, and became a human supremacy terrorist organization in ME2. They try and smooth it over, but you can tell that the two interpretations of Cerberus as an organization aren’t completely compatible. There’s no indication that Cerberus is more than a loose affiliation of soldiers in ME1, but in ME2, they have their hands in just about every pie and are this galaxy-spanning organization. That infrastructure is completely absent in ME1 while being taken as a given in ME2 and ME3.
Cerberus got its prominence seemingly mostly as a result of them being an outside agent from the Council and the Alliance who are responsible for resurrecting Shepard. But really… What was the point of Shepard’s death? I mean, I’ve touched on that subject before, how it bothers me how little the fact that Shepard is killed and resurrected actually MATTERS in the game, so considering that, why did they DO this? Okay, I get it on a level of ‘allowing a skill reset,’ given the massive alteration of the powers and skill trees between the games and all the other overhauls between the games, but… After making it a plot point, they don’t DO anything with it, and it results in a plot point that ends up being more severe story stall than anything else.
Cerberus’s primary existence in ME2 seems to be in order to provide a foundation for an antagonist for ME3. And there’s evidence that they failed miserably with that, given how many people seemed to want to say 'screw the Alliance’ in ME3, getting mad that Shepard ended up back in the Alliance by default in ME3. They portrayed Cerberus in a positive enough light that a lot of people came to embrace them.
And the problem with that stall is that Mass Effect, as a trilogy, does not recover from it until 3. One whole game is really nothing more than a stall, spinning the wheels because they’re saving 'the big guns’ for the grand finale. In fact, aside from Ashley/Kaidan having trust issues with Shepard about their ties to Cerberus, that alliance is little more than a footnote in the game proper - why are Ashley/Kaidan the only ones questioning Shepard’s association with Cerberus? Why doesn’t anyone else wonder about Shepard’s loyalties? The crew from ME2 are either absent, welcomed back to the Alliance with barely a comment, or simply say 'that wasn’t the Cerberus I joined,’ effectively distancing all the characters we’re supposed to like from their ties to Cerberus because ME3 requires them to be boogeymen.
What I end up seeing with the series is that they had two parts of a story they then decided to stretch into three parts. And what’s really sad is that there WAS an easy 'middle part’ for them to play with.
Let’s look to the magical world of 'what if.’ Instead of ME2 opening with the Normandy attacked by the Collectors and Shepard getting killed, ME2 opens with the Council and the Alliance forcing Shepard’s crew to be split up - Ashley/Kaidan get a promotion and reassignment, Tali returns to the Migrant fleet, Liara’s theories on the protheans are proven right so she’s getting her pick of archeological digs where she can find information on the protheans and now focus on what preparations they made for the Reapers, Garrus ends ME1 saying he’s going back to C-Sec, and Wrex is using his prominence to kick the krogans into line about doing something about the genophage. Shepard may or may not lose the Normandy, but either way, their crew is gone, scattered to the winds, out of direct face-to-face contact with Shepard.
But the Reapers are still out there.
And so ME2 becomes about dealing with the actual preparation and groundwork for the invasion, which means forging alliances preemptively, making sure they have the resources to stand against the Reapers (combat training for troops, material for ships, weaponry to fight them), and finding proof to convince politicians with their heads in the sand that Sovereign was not an isolated incident. It’s actually got elements in ME2, but instead of this being a Cerberus mission, with Shepard resurrected, Shepard’s instead gotten kicked upstairs, flying a proverbial desk (maybe getting some Spectre assignments, but they’re really simple stuff) and some of their skills are now rusty, and this is Shepard getting tired of being ignored and trying to be preemptive.
This time, instead of going on 'the Suicide Mission,’ the team that gets drawn in working with Shepard are some of the best operatives and agents that the non-human races have to offer as Shepard attempts to persuade their governments to stand together - if the point of Shepard’s ME2 mission is to get irrefutable proof that the Reapers are coming, then the grand finale could be facing one of the Destroyer variants of the Reapers, proving there’s more of them out there. HERE’S where we get to have the chance to first visit the various homeworlds - Shepard is making a direct appeal to the planetary leaders, rather than the Citadel Council, because the councilors ultimately answer to them, make connections with their populations. Meanwhile, thematically, we get to visit and make connections to the planets and it gives the invasion of those worlds in ME3 mean something when they fall.
You want antagonists? Focus with the Collector ships, rather than the base, make destroying one a set piece of the finale or something, and they can remain the antagonists, with the base saved for an element of ME3 - if we forge an alliance with the krogan and other races in the second game without necessarily curing the genophage, destroying the Collector base could be the objective of ME3’s first act. Or give the merc gangs more organization. Hell, make the batarians a threat, or perhaps even take advantage of the element of indoctrination and have a threat come from a Reaper-worshiping cult movement, a sort of higher functioning version of the machine cultists from a couple of sidequests, making the Reapers want to try subtlety in their attempt to reach into the galaxy since the keeper signal and Sovereign failed.
This also keeps Ashley/Kaidan out of the plot because they’re assigned elsewhere and would be disobeying orders to join Shepard on this mission, with the added bonus that they don’t end up spending a game and a half either absent or at odds with Shepard, possibly offering some behind the scenes assistance, and Liara could be too busy on her digs, on the trail of something big (and acting as a lead in to a DLC like in the game as is, or just something like the Crucible, allowing some actual foreshadowing of it) but still able to pass along information to Shepard. Wrex and Tali’s involvement can be about the same (Tali not joining immediately because of the need for her on the Haestrom mission, rather than specifically because of Cerberus), and Garrus can actually build off of the lessons he learned in ME1, about the importance of working WITH rules and regulations, rather than turning the lesson he got in the first game into lip service because of how he got tired of the rules and regulations at C-Sec. Plus his C-Sec connections make him a good liaison for Shepard’s mission.
Hell, if you really WANT Cerberus involvement, keep Miranda and Jacob as Cerberus Operatives, and here, they’re coming to Shepard with information about the Reapers, hiding their Cerberus ties until Shepard is committed to the mission they’re providing. Cerberus doesn’t even have to be a human supremacy movement in this version. It could - strengthen some ties to Terra Firma, for example, maybe showing it turning to embrace human supremacy, as opposed to already be about it, but Cerberus doesn’t need the prominence it got in the story.
Mass Effect’s big problem was how they wanted to do a trilogy, but they didn’t break the series as a trilogy. So they just tossed things at the wall for 2 and then let what stuck carry over into 3. ME2, for me, is the weakest of the series, in large part because as colorful as the characters are, they are not vital to the overall narrative. Part of that, of course, is the way things fell as a result of the Suicide Mission creating so many variables, the writing of the ME2 squad in ME3 wound up being so that they could easily be removed without damaging the plot. But it also impairs the story as a result, since it’s a story that has only the most tangential ties to the overarching plot.