Look, booh, fact is, its just a movie. A comic book movie. So the 80's sensibilities to be brought back in SR just to fit the story told in STM and SII is stretching it. You can just as easily say that all three movies take place in an alternate reality from ours (WHOAH!). Never mind the 25 years between the films. In the end of the day, that doesn't really matter.
Anyway, I agree with you about the mother scenes. I think we can have both Cal-El/Lara-El and Jor-El/Cal-El scenes brought back in. However, Jor El's time must be dominant. I say use her only on the Clark scenes, and not the other ones, the Luther scenes and so on.