The MJ story was pretty solid. I like the idea of her having a rival.
The idea of multiple artists for different narrative strands generally worked.
The Mysterio fake-out seemed a bit unnecessary, although I could see that some might think it's important to give the character an impressive moment when he's the main villain in the movies and someone else's lackey in the comics.
The Lizard epilogue seems a bit padded after a twelve issue saga. Those beats made more sense there. And it ended up taking Peter a really long time to decide whether he still wants to be in grad school.