Annoying Video Game Helper: There is no way to turn off Madame Web's hints. Reaches insane levels during the Sandman boss-fight where she'll continuously tell you to find something in the debris and to use water-barrels, often in rapid sucession. Over and over.
Anti-Climax Boss: It's absurdly easy to button mash Electro to death in the DS version without him so much as lifting a finger.
Venom is not in the game, though Carnage is. Justified since Ultimate Spider-Man already has the symbiote.
For some, the presence of symbiotes themselves annoyed them, as between Ultimate Spider-Man, the Spider-Man 3tie-in game, and Web of Shadows, they were fatigued about symbiotes and wanted a break from them, whereas others understood why Ultimate Spider-Man was in the black suit (mainly to keep his gameplay different from Amazing Spider-Man) and accepted it.
Complete Monster: Mysterio (Quentin Beck) is the Big Bad of the game, and is portrayed as far more wicked and dangerous than in the comic. Failing to steal the Tablet of Order and Chaos due to Spider-Man's interference, Mysterio escapes with one of the now-shattered fragments of the Tablet. Realizing the power of his fragment, Mysterio goes on a rampage, destroying anything in his path. After finding Madame Web's location, Mysterio tortures her, then uses her as a hostage to force Spider-Man to retrieve the rest of the Tablet's fragments for him. Restoring the Tablet to its original state, Mysterio gains god-like powers, destroys the Multiverse, and plans to remake it in his image.
Good Bad Bugs: The Wii version allows you, in the Noir Stages, to rescue a hostage fairly quickly in the Goblin segment by simply walking through the right bars (also meaning you don't need to open the cage in the first place.). A similar glitch is also in the first level, and requires some timing to pull of, which allows you to get in the hallway Hammerhead and his henchmen are: Get spotted, and then use a web-strike, and you'll be in the same hallway, though they'll have disappeared. Doing so, however, means that you will be unable to progress in the level and have to restart.
Marvel had previously claimed that a crossover between the mainstream and Ultimate books would mean they had officially run out of ideas. This has mainstream, Ultimate, 2099, and Noir!
Even better; in later years the Ultimate Universe would crossover with the regular 616 one several times, finally culminating in Secret Wars II, when the two universes annihilate each other. The subsequent reboot did away with the Ultimate universe altogether, while bringing some of it's characters, like Miles Morales, into the 616 universe.
One of the commercials in the Pain Factor level is a Blaxploitation themed advert for Stephen Strange, Jr, the Ultimate Dr. Strange. Becomes this with the line "He's cheated death itself," given that by the time the game was released, Strange Jr. was dead.
They Wasted a Perfectly Good Plot: A pre-order bonus is Cosmic Spider-Man suits for the four different Spidey's, the endgame features Mysterio trying to destroy all four universes... Yet somehow, the Cosmic Spidey costumes weren't worked into the storyline.
It's weird that in the Spider-Man Noir segments, The Kingpin isn't the final boss considering how perfect he would've been for the segment.
To an extent, there's the fact that none of the Spider-Men ever interact with each other outside of the final boss fight. Edge of Time would rectify this a bit with constant dialogue between Amazing and 2099.
WTH, Casting Agency?: Dan Gilvezan as 2099. While he gives a humorous performance, the age in his voice is quite apparent, especially when compared to the more appropriate voice 2099 would get in Edge of Time.