Regarding the fact that this movie takes more liberties to change aspects of the characters origins than most recent Marvel films have, this has a lot to do with the fact that the Spider-Man movie franchise is owned by Sony and not by Marvel. Iron Man, Hulk, Captain America and Thor are all owned by Marvel, and the movies are made by Marvel Studios, which means that Marvel has total control over those characters.

Regarding Mary Jane, don't forget that Peter didn't yet know her while in high school in the comics. His first love was Gwen Stacey. So in this particular case, this movie is closer to the comics than previous films had been.