As far as am concerned the only canon is everything after/during mk9.
that's like saying the stuff before the new 52 is canon.
what's the point of rebooting if it doesn't reset the story and what we know about the lore?
Well, the point was to basically sell a lot of games around the world by creating the same atmosphere from the original games!!
They had to come up with a way to revive all dead characters and re-create that situation and, as a lot of media has done lately, chose the time travel/reboot thing.
But they can't change the past. What do you mean all is cannon is after/during MK9? That's absurd.
Where does Raiden come from? Is he just another guy with a funny hat who woke up in the story? No. He's the God of Thunder as has been the Protector of Erathrealm for thousands of years. That's where he comes from.
Who's Kitana? Kahn's real daughter? Kahn's step daughter adopted 20 years ago after he conquered Edenia? No, she's his 10.000 year old daughter. Edenia was conquered 10.000 years ago.
EVERYTHING in the lore still remains. The writers even confirmed that, besides a few inconsistencies, everything that happened in the past is unchanged.
In fact, it wouldn't make sense to change it, as the current story derives from that.