Oh...I completely disagree. There would be ways to fit the story around the players past choices. I don't want my choices and my characters from the past games to simply be discarded like they never existed.
I agree that choices should remain, but think it a bit melodramatic to think in terms of a canon storyline somehow destroying your choices from the first two. Of course, if you've only played either of the first two games once or twice (1 LS/ 1 DS), then perhaps this might be a hangup for you. I've played them enough times that canon wouldn't give me fits of apoplexy, but would still manage to be a wee bit stifling.