Spider-Man 2 has a special place in my heart, but even I have to admit that the crap you had to do in the part with Mysterio is retarded. The obstacle course was annoying because in order to complete it, you had to be very comfortable with the controls because they were fairly clunky and awkward.
I wouldn't consider that a mini-game because it was part of the main plot, but you are definitely right. It was incredibly annoying and almost made me quit the game.