I believe you can kill all your companions in Skyrim if is not
their quest. I don't like using it as an example, I don't want 99 more games identical to Skyrim. Once again though, Skyrim did not advertise itself as starting off where you left off in Oblivion and have decisions that impact the game.
Our whole discussion about events in ME is irrelevant to the point I was (possibly poorly) making, I was pointing out how I felt, and could see my roomate felt frustration with characters and he thought he would be able to kill them from what he had heard about the game. But, my main problem with the series (and what makes me feel alienated) is the plot being so far from what was advertised for ME2 as far as choices.
The first game behaved appropriately, assuming more DLCs came out for it it, but I dont fault Bioware for that either. It had the potential to branch out into multiple story-lines.
Enters ME2:
Nothing effected the storyline of the game, it was a farcry from what it was supposed to be (Kind of like Far Cry 2 but more fun).
I don't believe the proposition that you cannot build plot development in a game where main characters die dynamically. They sure could, have multiple voice actors speak the dialog for main parts. Let your players kill all their companions.
What I am suggesting (I warn you its pretty rough but you get the idea)) is as easy to implement as Shepard endorsing a store. Throw in missions like that for everything, to determine if your companions get along or not. What I suggested is a game-world changing event, but it does not have to effect the main plot. Bioware has the right idea, they are just doing it wrong. The Rachni are an example of this, a conversation based upon what was supposed to be a large decision?
ME2 is linear and it was advertised as not being liner. It was designed to be a safe game investment, safe and non-linear do not work together.