I'm not sure I agree about the Legion's mission response there. It's true that it's not a simple yes/no situation, but the process could be this: Did the Player use Legion as a Character Y/N, If Yes did they Reprogram the Geth or Destroy them, R/D. Thus allowing for 3 contingencies, 1: you Reprogram, 2: You destroy, 3: you didn't use Legion, therefore the Geth remain unchanged from either of the above.
They've had situations in the carryover from ME1 that worked in a similar fashion, albeit on a smaller scale. My Male Shepard from ME1 either A: Romanced Liara B: Romanced Ashley or C: Neither or the one pursued died at Virmire. At the beginning of ME2 it would go like this, If A is True, Liara runs to see Shepherd during the attack. If B is true, Ashley runs to see Shephard during the attack. If C is true, Kaiden runs to see Shepherd during the attack.
It's been said that they are using a thousand different points to carry over from ME2 to ME3, The loyalty missions like Mordins probably will have some impact.