Surprisingly, Mary Jane's presence in the game, with her and Peter still being together, was met far more warmly than one might expect. Probably because, instead of following the current post-One More Day comics and using CarlieCooper, the game's developers stuck with the more traditional, and far more favored pairing. Her being voiced by Supergirl didn't hurt either.
Good Bad Bugs: In the Wii version, by punching the air in the time-gate room after you beat the first phase of Anti-Venom as Amazing Spider-Man, Amazing's lines and quotes will act like Anti-Venom is still in the room, despite him being launched into another room.
Hilarious in Hindsight/Harsher in Hindsight: One of the available outfits is the suit used by Miles Morales, Peter Parker's successor in the Ultimate Universe. Flash-forward to 2012, where the 616-verse Spider-Man finally gets to meet him.
...That's not true. For the sake of accuracy, the free-roamers did do well. Spider-man 2, Ultimate Spider-Man, and Spider-Man: Web of Shadows all rated above average, and were all well received by fans.
They Changed It, Now It Sucks: People have complained that Spider-Man's costume is ruined by the webbing, since it looks off... It's because the character designers have deviated from the classic design and made the webbing pattern uneven, like an actual spider web.