Although is still one of the best games in 2012, the game confused and split fans and generally most players tried it.
- WARNING: Following, Contains Spoilers -
A game is nice to have a story and, in this case, some mystery and twists too. But since ME3 is the end of the trilogy, devs ought to give a solid one. Leave questions for the future? Fine. But leave questions during game and for the structure of the game story, is poor. I see people arguing about what happened. Some want "indoctrination", some other an "is-all-explained" and goes on. I don't know and really don't care which one is true. After 5 years and lot's of installments (=money), i see no reason leaving intentionally "plot holes" so the gamers start "conspiracy theories". This is not a historical event, is A SCI-FI GAME, and it ended. So, imho, Bioware just failed (intentionally or not), to deliver a decent end to the plot.
I think the best review of the game is the following video. Is bit long, about 40 mins, but explains how such a game should work and progress. The video isn't mine, i don't even know the person who did it. But after seen some videos of people moaning or praising, i really think that this one is 100% accurate.
Contains a lot of spoilers, so if the game is new to you and want to play it, avoid it until you done playing.
https://www.youtube.com/watch?v=7MlatxLP-xs