Some of the choices you mention would have caused Bioware to make completely different games.
For example if the Citadel Council sends teams to the Collector base, they'd not be caught unaware by the Reaper invasion and the entire storyline for the first act of the game would have to be rewritten.
Just think about it, the sequels have to begin at the same point, which also means that ME1 and ME2 both have to end at the same point as well. And yet there are many small differences - I still wonder how they're going to handle lost squad members in ME3. What if you lost Mordin, who's gonna be there on the salarian homeworld? What if you didn't even reactive Legion, how are you going to get that geth mission seen in the E3 demo? It's already a lot of extra work that Bioware was willing to put into the game, just think about all those players who made different choices in ME2 and won't get these scenes.
I think there was an interview with Casey Hudson where he talked about these issues and also mentioned that ME3 is where they can finally start to diverge from a single plot thread. Maybe if you didn't reactivate Legion, you won't have a chance to settle the quarian-geth conflict at all and the entire migrant fleet will be destroyed... and so on.
Oh man, you've not been a GM for 10 years, trust me, if I want my PC to go somewhere, I'll find a way, I'll move locations to put them on their road, I may change the events a little but it's NOT difficult to do as you like and give illusion of freedom. Just ask any experienced Game Master.
As a simple exemple, in SHOGO your brother is a rebel and your father represents order, but depending who you side with the other is either a terrorist or a dicator, respectively.
The story changed, but the missions don't have to, the reason why you do them and the opponent changes, not the gameplay itself.
What's important is that the story unfolds differently, but you can still reuse a lot in the process. (Otherwise every GM out there would be overwhelmed after a few minutes in a game, as PC are typically unpredictable, yet all manage to get the story unfold one way or another.)