You see, I like the potential paradigm shift that occurs at the very end. I like the fact that the Illusive Man's fundamental philosophy can be interpreted as something positive. When you strip away all of Cerberus' immoral experiments and all the racism, you are left with a philosophy which encourages the exploration of new frontiers. We
should embrace new technology. We
should investigate that which we do not understand. We
should dispel Lovecraft's fears. We
should venture into the unknown. We
should illuminate the dark places.
The problem is that these ideas were not presented effectively. The writers did not justify the Control and Synthesis options. Destroy is the only viable choice for many people, and that's a real shame. It doesn't help that each choice seems to validate certain unpleasant perspectives.
[/quote]
Okay, I hope this won't be a wall of text, but there are too many points to address in a few short sentences. I'm not saying IT was the end all be all, but BioWare and EA clearly had a fire storm on their hands, and what IT does offer is that it is a _major_ theme of the games. IT was presented as a grave threat all the way back with Liara's mama. That means it met one essential criteria for good writing in that it had been _set up_.
This comes back to the issue of keeping the promise to your reader/viewer/player that you make in the beginning. You better keep that contract or woe betide. There's a big blog post about that too on my blog. It was done perfectly in Dragon Age: Origins. And let me offer an example from one of my novel series. A Prometheus character tells my hero that if we follow his path he will "give us the stars". I better pay that off or my readers are not going to be happy with me, and rightly so.
I also think the third game suffered by not having an identifiable antagonist. Yes, they tried to make TIM a personalized opponent, but it felt very forced, and I kept finding myself asking uncomfortable questions that pulled me out of the game. To wit -- how on Earth was Cereberus able to afford mounting these armies? And why would humans be fighting each other and not the Reapers? Yes, TIM and Kai Leng were indoctrinated, but presumably not every Cerberus soldier was.
In the beginning I wanted to like The Illusive Man -- I mean it was President Bartlett,

but at it's core Cerberus is presented to us from the first game as a racist and utterly immoral organization. They make that clear in one of Shepard's origin stories. And doesn't the Alliance encourage exploration? It's sort of the Star Trek Federation, except people had flaws which made them more interesting. Point is by the middle of the third game I despised TIM and all he stood for. I could not pick control.
Personally I found all three of the choices offered at the end to be horrific for varying reasons, and I also find the option of a "happy ending" to be perfectly acceptable and was disappointed that it wasn't offered. (I wrote a long blog post about the efficacy of happy endings and why I think they come in for a bad rap. People can go find it if they're interested.) Point was that by the time it was over there wasn't a sense of choice at all, and no opportunity for the falling action and resolution scene that people need or the story feels incomplete. The EC tried to address that, but I found it lacking. It was adequate voice over and a few slides. Not worthy of something this epic.
But ultimately it comes back to structure -- the Catalyst was never hinted at in game one or in game two. For that matter neither was the Cruicible. When something comes out of nowhere it can't feel organic and it feels like the writers are just starting to make it up as they go along. At that point the reader/viewer/player starts to lose confidence, and you're going to lose them. You can't introduce a new antagonist in the final 10 pages or 10 minutes. It seems that almost every player viewed the Catalyst with disapprobation and as a villain and therefore they felt whip sawed. It was clear that Harbinger needed to be the ultimate opponent in game three, the stand in for all his kind, but he was singularly absent from the game.
Finally, there's the issue of theme. All through the games Shepard is building concensus while still allowing people to keep their individuality as a person and member of a particular species. I really thought the writer's were going to have the alliance you build be the ultimate solution. They even partly set it up in a conversation with Javik. He talkes about how there was no alliance in his time because the Protheans were conquers. They had no true allies. There could have been real consequences if you killed the Rachni queen, etc. etc. but none of it mattered.
I suppose you could make the argument that synthesis is about unity, but it's a forced unity and so I found it abhorrant too. I wanted a clean win where the galaxy says -- "Not this time" and that was not offered. I go back to Dragon Age: Origins. The players get to craft a solution to the problem of the archdemon that works for their particular Grey Warden. Nobody suddenly told me I had to become a darkspawn, or become the archdemon and control the darkspawn. They paid off the promise made at the end of the first 30 minutes of play -- that Allistair and I are going to go into the world, forge alliances and save Ferelden from the darkspawn. I wanted that for Mass Effect.