Really I wouldn't consider Mass Effect 2 letting you kill off pretty much everyone a small variation.
Not to mention Mass effect letting you kill the council and have humanity take control of the galaxy is kind of a major thing.
In-universe, they're big. But in the narrative as presented, they don't make much of a difference. It doesn't matter who the Council is in ME3. It doesn't matter which squad members you let die in the last two games - they'll have a replacement. It doesn't matter if you killed the rachni - they're magically back.
There's no substantial difference in the flow of the narrative based on your choices in the first two games. Or indeed even during the third.