There is choice in Mass Effect, but ultimately, Bioware wrote the story and the choices. The player does not have complete control over what happens in the game. I mean there's lots of choices to pick from, but ultimately you have to deal with what's been programmed into the game.
It's like that with any game. If you wanted a particular type of ending, but it wasn't programmed into the game, then you have to deal with the confines of the game's design.
There's only so much control the player has. I mean there's quite a bit of control they give you, but some people still think this is *their* story, and *their* choices, and *their* character. It's not. The developers ultimately hold the cards since they developed the characters. worlds, sound effects, dialog, etc.