It's not the worst story ever, but it's the most disappointing plot I've experienced in years - Mass Effect 2. In fact, considering the emphasis the series places on narrative, and Bioware's reputation for crafting story-driven "RPGs", it's astounding that ME2 had such an atrocious main story that eviscerates the overarching plot for the entire series. I mainly took issue with a few details -
Cerebrus & Shepard's Death- Going from the evil organization in the first game to an organization whose noble ideals are befuddled by questionable actions was a huge retcon that I still have trouble accepting. Shepard's death event can be attributed to Bioware wanting Shepard to be tied to Cerebrus at best, and as a lazy instance where gameplay requirements (class reset) influence the story at worst. Following the resurrection, Shepard's given no choice in the matter of joining Cerebrus (there is the typical Biowarian illusion of choice where saying "no" does nothing). Despite Shepard's actions of thwarting Cerebrus' plans in the first game, The Illusive Man makes no mention of those events, which was jarring. Furthermore, by taking the "Sole Survivor" background in the first game, Shepard's squad was wiped out by Cerebrus' actions, and a juicy confrontation stemming from this event is conspicuously absent.
Shepard's resurrection was a giant missed opportunity as well. On the other end of the plot spectrum, Planescape Torment shows how much potential such a plot device has, but ME2 treats it as largely inconsequential, with Alliance Officers and other important characters brushing away the issue after a single line or two. Shepard ends up with a similar body, ship and ship crew as compared to the first game following the resurrection, with the only difference being Cerebrus' name printed on the side of his ship - a profoundly stupid thing to do considering the reputation the organization has. But then again, like most choices in the Mass Effect universe, this lacks the expected consequence of Alliance Officers treating Shepard as an adversary when the Normandy docks at a space station.
Reapers and Collectors - The Reapers went from being a cold and calculating machine species to having their mysterious aura taking a beating due to the bungling actions of their minions, the Collectors. Introducing the Collectors as a new threat midway through the trilogy was a questionable decision, especially so when the Reapers have already been shown to be intimidating adversaries with their presumed limitless numbers.
Which brings me to their supposed intent to harvest millions of humans to construct a human reaper. Following the utter disdain the Reaper from the first game shows towards organics, this sudden plot detail was illogical - even more when a single Reaper is not enough to win the war, as the first game showed. All in all, it seems like a lazy attempt to inject some drama by having human abductions, which will presumably cause the player to want to take down the collectors. That, and having a cartoon villain named Harbinger spewing stereotypical villainous one-liners. Meanwhile, the Reaper story scarcely makes any headway since where it left at the end of the first game.
The Suicide Mission Setup - ME2's main plot was spread paper-thin across the whole game, but the much hyped-up plot development that is foreshadowed from the very beginning is the supposed "suicide mission." In fact, it seems that the entire game's plot developed from this central suicide mission idea, which would explain for how little main plot there is in the game. Unfortunately, I couldn't take it seriously when my *entire* party boarded the shuttle for no reason, leaving Normandy defenseless and the ship's crew vulnerable to being kidnapped. I realize that this was done to instill a sense of urgency into the proceedings, but the utter hilarity of my entire squad being crammed into a tiny shuttle for no reason was only surpassed by my incredulity at Bioware's writers not noticing how idiotic it is for all of Shepard's party to board the shuttle after refraining from doing so over two games. This was when I began to appreciate that ME2 had as little main story as it did, since more plot developments of this caliber would have left me senseless.
The Final (frustratingly binary) "Choice" - If there's one instance in a Bioware game that exhibits the idea that Bioware's handling of choices in WRPG games is lackluster compared to Black Isle/Troika/Obsidian/CDPR games, it's this one. Shepard is faced with the dilemma of blowing up the collector base, or handing it over to Cerebrus, when the logical option would be to hand it over to the Alliance instead. By doing so, the tired plotline that carries over from the first game - the Alliance not believing the Reaper threat - can be finally resolved, and research can be done to combat the Reaper threat using their own technology. The millions of humans who were abducted could also be identified based on their unused bodies, paving the way for their families to be notified. Instead, we are faced with a dung-brained Shepard taking the moral high-ground on the basis of not wanting to "sacrifice the human species' soul" nonsense.
There are other numerous plot holes and retcons, like the ammo clips making a comeback and magically appearing during Jacob's loyalty quest, Mordin inexplicably gaining possession of a Collector bug and Ashley meeting with Shepard after it seemed she was in the process of being abducted, which all effectively made me want the game to end so that I could be done with the brain hurt the numerous plot inconsistencies were causing. As a result of ME2's plot, humanity's supposed "special" status and Shepard's transformation into the galaxy's sole hope, akin to Master Chief and Gordon Freeman, I have no hope for ME3's story at all.