I have very mixed feelings about Mary Jane Knowing All Along.
On the minus side, I'd have preferred it if she'd figured it out, through a series of clues, and put at least some amount of guess-work into it, because it'd give her a leg up on Lois Lane, The World's Worst Investigative Reporter.
On the plus side? If you didn't know that Peter was Spider-Man, the way he behaved toward most of the folks around him would have seemed pretty prickish in those days, so it's actually a lot more respectful toward Mary Jane to establish that she knew he was Spider-Man back then, because otherwise, you've got the story of a woman who's putting up with all sorts of bullshit from an apparent asshole for no real reason at all.