^I rather think if you didn't use Legion then the heretics would have used the virus and converted the other side to their mindset. I'm not saying they won't have an effect, i'm sure there'll be a ton of stuff that carries over, large and small, but I can't see them stacking the deck so that a decision in ME1 or 2 could make it impossible to (for lack of a better term) "win."
I probably wasn't articulating my thinking very well, but in a nutshell, what I was getting at was that I'm pretty confident that the only effect such things as the status of the Geth, Quarrians, Rachni, Krogan etc. will have is the general state of the galaxy when all the dust settles (think along the lines of the epilogue in Dragon Age.)
To give a hypothetical example, if you killed the Rachni queen then you have less forces on your side to fight the Reapers, so while you may defeat them, Earth suffers greater casualties. Or for another if you let the council die on ME1 then let the Illusive man have the Collector base then humanity may become a tyrannical and oppressive force throughout the galaxy, using Reaper tech to assert dominance over all the other races and build a human empire.
Both of these hypothetical scenarios of course would have a massive impact on the galaxy at large but not the plot of the game itself (as opposed the the narrative.) Think about the impact ME1 had on ME2: did it really make much of a difference to the plot if you saved Kaiden or Ash? Did talking Wrex around or killing him affect your ability to secure Grunt's loyalty? No. Indeed nothing you did in ME1 altered the plot for ME2. Sure there's tons of details that can change, characters like Fist, that Asari commando from Feros or that undercover cop from Noveria that can crop up based on what you may or may not have done but that only effects the narrative. The plot of the game was: Shepard died -> Cerberus brought him/her back -> Collectors are abducting humans so build a team and go stop them.
Nothing you did in ME2 changed any of that and likewise I don't think anything will drastically affect the plot of ME3, only vary the narrative. Just from a practical standpoint, if even a handful of events could radically change the plot then they'd basically have to make several different games to account for all possible permutations with whole levels and missions rendered inaccessible depending on the character import.
While we're on the subject, let's take a look and try and figure out the framework ME3 would have to work in based on decisions from ME2. Firstly, since and any all of the companions could potentially die, there can't be anything in ME3's plot that would require any specific individual's presence. So in all likelihood your companions will be taken away from you regardless...which is probably what'll happen anyway since they'll need to wipe the slate clean to start a new game.
I can't help but wonder how they'll do that since there's no way you should start a new game with all of your weapons, armour, upgrades and abilities that you has by the end of ME2. It's not as if they can just blow up the Normandy again...one hopes.